This invention relates to newly identified polynucleotides, polypeptides encoded by these polynucleotides, antibodies that bind these polypeptides, uses of such polynucleotides, polypeptides, and antibodies, and their production.
Unlike bacterium, which exist as a single compartment surrounded by a membrane, human cells and other eucaryotes are subdivided by membranes into many functionally distinct compartments. Each membrane-bounded compartment, or organelle, contains different proteins essential for the function of the organelle. The cell uses xe2x80x9csorting signals,xe2x80x9d which are amino acid motifs located within the protein, to target proteins to particular cellular organelles.
One type of sorting signal, called a signal sequence, a signal peptide, or a leader sequence, directs a class of proteins to an organelle called the endoplasmic reticulum (ER). The ER separates the membrane-bounded proteins from all other types of proteins. Once localized to the ER, both groups of proteins can be further directed to another organelle called the Golgi apparatus. Here, the Golgi distributes the proteins to vesicles, including secretory vesicles, the cell membrane, lysosomes, and the other organelles.
Proteins targeted to the ER by a signal sequence can be released into the extracellular space as a secreted protein. For example, vesicles containing secreted proteins can fuse with the cell membrane and release their contents into the extracellular spacexe2x80x94a process called exocytosis. Exocytosis can occur constitutively or after receipt of a triggering signal. In the latter case, the proteins are stored in secretory vesicles (or secretory granules) until exocytosis is triggered. Similarly, proteins residing on the cell membrane can also be secreted into the extracellular space by proteolytic cleavage of a xe2x80x9clinkerxe2x80x9d holding the protein to the membrane.
Despite the great progress made in recent years, only a small number of genes encoding human secreted proteins have been identified. These secreted proteins include the commercially valuable human insulin, interferon, Factor VIII, human growth hormone, tissue plasminogen activator, and erythropoeitin. Thus, in light of the pervasive role of secreted proteins in human physiology, a need exists for identifying and characterizing novel human secreted proteins and the genes that encode them. This knowledge will allow one to detect, to treat, and to prevent medical diseases, disorders, and/or conditions by using secreted proteins or the genes that encode them.
The present invention relates to novel polynucleotides and the encoded polypeptides. Moreover, the present invention relates to vectors, host cells, antibodies, and recombinant and synthetic methods for producing the polypeptides and polynucleotides. Also provided are diagnostic methods for detecting diseases, disorders, and/or conditions related to the polypeptides and polynucleotides, and therapeutic methods for treating such diseases, disorders, and/or conditions. The invention further relates to screening methods for identifying binding partners of the polypeptides.
Definitions
The following definitions are provided to facilitate understanding of certain terms used throughout this specification.
In the present invention, xe2x80x9cisolatedxe2x80x9d refers to material removed from its original environment (e.g., the natural environment if it is naturally occurring), and thus is altered xe2x80x9cby the hand of manxe2x80x9d from its natural state. For example, an isolated polynucleotide could be part of a vector or a composition of matter, or could be contained within a cell, and still be xe2x80x9cisolatedxe2x80x9d because that vector, composition of matter, or particular cell is not the original environment of the polynucleotide. The term xe2x80x9cisolatedxe2x80x9d does not refer to genomic or cDNA libraries, whole cell total or mRNA preparations, genomic DNA preparations (including those separated by electrophoresis and transferred onto blots), sheared whole cell genomic DNA preparations or other compositions where the art demonstrates no distinguishing features of the polynucleotide/sequences of the present invention.
In the present invention, a xe2x80x9csecretedxe2x80x9d protein refers to those proteins capable of being directed to the ER, secretory vesicles, or the extracellular space as a result of a signal sequence, as well as those proteins released into the extracellular space without necessarily containing a signal sequence. If the secreted protein is released into the extracellular space, the secreted protein can undergo extracellular processing to produce a xe2x80x9cmaturexe2x80x9d protein. Release into the extracellular space can occur by many mechanisms, including exocytosis and proteolytic cleavage.
In specific embodiments, the polynucleotides of the invention are at least 15, at least 30, at least 50, at least 100, at least 125, at least 500, or at least 1000 continuous nucleotides but are less than or equal to 300 kb, 200 kb, 100 kb, 50 kb, 15 kb, 10 kb, 7.5 kb, 5 kb, 2.5 kb, 2.0 kb, or 1 kb, in length. In a further embodiment, polynucleotides of the invention comprise a portion of the coding sequences, as disclosed herein, but do not comprise all or a portion of any intron. In another embodiment, the polynucleotides comprising coding sequences do not contain coding sequences of a genomic flanking gene (i.e., 5xe2x80x2 or 3xe2x80x2 to the gene of interest in the genome). In other embodiments, the polynucleotides of the invention do not contain the coding sequence of more than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5, 4, 3, 2, or 1 genomic flanking gene(s).
As used herein, a xe2x80x9cpolynucleotidexe2x80x9d refers to a molecule having a nucleic acid sequence contained in SEQ ID NO:X or the cDNA contained within the clone deposited with the ATCC(copyright). For example, the polynucleotide can contain the nucleotide sequence of the full length cDNA sequence, including the 5xe2x80x2 and 3xe2x80x2 untranslated sequences, the coding region, with or without the signal sequence, the secreted protein coding region, as well as fragments, epitopes, domains, and variants of the nucleic acid sequence. Moreover, as used herein, a xe2x80x9cpolypeptidexe2x80x9d refers to a molecule having the translated amino acid sequence generated from the polynucleotide as broadly defined.
In the present invention, the full length sequence identified as SEQ ID NO:X was often generated by overlapping sequences contained in multiple clones (contig analysis). A representative clone containing all or most of the sequence for SEQ ID NO:X was deposited with the American Type Culture Collection (xe2x80x9cATCC(copyright)xe2x80x9d). As shown in Table 1, each clone is identified by a cDNA Clone ID (Identifier) and the ATCC(copyright) Deposit Number. The ATCC(copyright) is located at 10801 University Boulevard, Manassas, Va. 20110-2209, USA. The ATCC(copyright) deposit was made pursuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for purposes of patent procedure.
A xe2x80x9cpolynucleotidexe2x80x9d of the present invention also includes those polynucleotides capable of hybridizing, under stringent hybridization conditions, to sequences contained in SEQ ID NO:X, the complement thereof, or the cDNA within the clone deposited with the ATCC(copyright). xe2x80x9cStringent hybridization conditionsxe2x80x9d refers to an overnight incubation at 42 degree C. in a solution comprising 50% formamide, 5xc3x97SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5xc3x97 Denhardt""s solution, 10% dextran sulfate, and 20 xcexcg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1xc3x97SSC at about 65 degree C.
Also contemplated are nucleic acid molecules that hybridize to the polynucleotides of the present invention at lower stringency hybridization conditions. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature. For example, lower stringency conditions include an overnight incubation at 37 degree C. in a solution comprising 6xc3x97SSPE (20xc3x97SSPE=3M NaCl; 0.2M NaH2PO4; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 ug/ml salmon sperm blocking DNA; followed by washes at 50 degree C. with 1xc3x97SSPE, 0.1% SDS. In addition, to achieve even lower stringency, washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5xc3x97SSC).
Note that variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt""s reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.
Of course, a polynucleotide which hybridizes only to polyA+ sequences (such as any 3xe2x80x2 terminal polyA+ tract of a cDNA shown in the sequence listing), or to a complementary stretch of T (or U) residues, would not be included in the definition of xe2x80x9cpolynucleotide,xe2x80x9d since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone generated using oligo dT as a primer).
The polynucleotide of the present invention can be composed of any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. For example, polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single-and double-stranded regions. In addition, the polynucleotide can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA. A polynucleotide may also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons. xe2x80x9cModifiedxe2x80x9d bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications can be made to DNA and RNA; thus, xe2x80x9cpolynucleotidexe2x80x9d embraces chemically, enzymatically, or metabolically modified forms.
The polypeptide of the present invention can be composed of amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain amino acids other than the 20 gene-encoded amino acids. The polypeptides may be modified by either natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Polypeptides may be branched, for example, as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. (See, for instance, PROTEINSxe2x80x94STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993); POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, New York, pgs. 1-12 (1983); Seifter et al., Meth Enzymol 182:626-646 (1990); Rattan et al., Ann NY Acad Sci 663:48-62 (1992).)
xe2x80x9cSEQ ID NO:Xxe2x80x9d refers to a polynucleotide sequence while xe2x80x9cSEQ ID NO:Yxe2x80x9d refers to a polypeptide sequence, both sequences identified by an integer specified in Table 1.
xe2x80x9cA polypeptide having biological activityxe2x80x9d refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the present invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. In the case where dose dependency does exist, it need not be identical to that of the polypeptide, but rather substantially similar to the dose-dependence in a given activity as compared to the polypeptide of the present invention (i.e., the candidate polypeptide will exhibit greater activity or not more than about 25-fold less and, preferably, not more than about tenfold less activity, and most preferably, not more than about three-fold less activity relative to the polypeptide of the present invention.)
Many proteins (and translated DNA sequences) contain regions where the amino acid composition is highly biased toward a small subset of the available residues. For example, membrane spanning domains and signal peptides (which are also membrane spanning) typically contain long stretches where Leucine (L), Valine (V), Alanine (A), and Isoleucine (I) predominate. Poly-Adenosine tracts (polyA) at the end of cDNAs appear in forward translations as poly-Lysine (poly-K) and poly-Phenylalanine (poly-F) when the reverse complement is translated. These regions are often referred to as xe2x80x9clow complexityxe2x80x9d regions.
Such regions can cause database similarity search programs such as BLAST to find high-scoring sequence matches that do not imply true homology. The problem is exacerbated by the fact that most weight matrices (used to score the alignments generated by BLAST) give a match between any of a group of hydrophobic amino acids (L, V and I) that are commonly found in certain low complexity regions almost as high a score as for exact matches.
In order to compensate for this, BLASTX.2 (version 2.0a5MP-WashU) employs two filters (xe2x80x9csegxe2x80x9d and xe2x80x9cxnuxe2x80x9d) which xe2x80x9cmaskxe2x80x9d the low complexity regions in a particular sequence. These filters parse the sequence for such regions, and create a new sequence in which the amino acids in the low complexity region have been replaced with the character xe2x80x9cXxe2x80x9d. This is then used as the input sequence (sometimes referred to herein as xe2x80x9cQueryxe2x80x9d and/or xe2x80x9cQxe2x80x9d) to the BLASTX program. While this regime helps to ensure that high-scoring matches represent true homology, there is a negative consequence in that the BLASTX program uses the query sequence that has been masked by the filters to draw alignments.
Thus, a stretch of xe2x80x9cXxe2x80x9ds in an alignment shown in the following application does not necessarily indicate that either the underlying DNA sequence or the translated protein sequence is unknown or uncertain. Nor is the presence of such stretches meant to indicate that the sequence is identical or not identical to the sequence disclosed in the alignment of the present invention. Such stretches may simply indicate that the BLASTX program masked amino acids in that region due to the detection of a low complexity region, as defined above. In all cases, the reference sequence(s) (sometimes referred to herein as xe2x80x9cSubjectxe2x80x9d, xe2x80x9cSbjctxe2x80x9d, and/or xe2x80x9cSxe2x80x9d) indicated in the specification, sequence table (Table 1), and/or the deposited clone is (are) the definitive embodiment(s) of the present invention, and should not be construed as limiting the present invention to the partial sequence shown in an alignment, unless specifically noted otherwise herein.
Polynucleotides and Polypeptides of the Invention
Features of Protein Encoded by Gene No: 1
The translation product of this gene shares sequence homology with alloreaction associated antigen (ARAg), or V7, a transmembrane protein with an extracellular domain containing 7 immunoglobulin like domains. ARAg is present on the surface of alloantigen activated CD8+ T cells, monocytes, granulocytes and peripheral dendritic cells and can be used to screen potential immunosuppressants, identify and isolate ARAg receptors and generate MAb for suppressing an immune response. A mAb directed against V7 inhibits the proliferative response of T cells to allogenic cells or immobilized anti-CD3 Ab, but not lectin mitogens, suggesting that V7 plays a role in TCR/CD3-mediated T cell activation. Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with T-cell activator proteins, and particularly V7. Such activities are known in the art, some of which are described elsewhere herein (See, for example, J. Immunol. 154 (9), 4434-4443 (1995); all the information available through this reference is hereby incorporated herein by reference).
A preferred polypeptide variant of the invention comprises the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 580-596 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 597 to 648 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ia membrane proteins.
This gene is expressed primarily in brain and primary dendritic cells and to a lesser extent in activated T cells, as well as several other tissues.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: neurodegenerative disorders; immune system dysfunction; immunosuppression; transplant rejection; graft versus host disease; inflammatory disorders; and autoimmune diseases. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the brain, CNS, and immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, immune, hematopoietic, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 82 as residues: Thr-52 to Phe-62, Pro-130 to Arg-135, Pro-160 to Arg-173, Thr-190 to His-195, Gly-246 to Arg-252, Arg-397 to Thr-403, Gly-414 to Arg-420, Arg-483 to Glu-488, Arg-525 to Arg-530, Gly-535 to Val-541. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in primary dendritic cells and activated T cells, combined with the homology to ARAg or V7 indicates that polynucleotides and polypeptides corresponding to this gene are useful for the diagnosis and/or treatment of a variety of immune disorders. Previous studies have indicated that V7 or ARAg is involved in T cell activation and in immune responses. Therefore, this gene may play similar roles, and may be involved in inflammation, autoimmunity, susceptibility to infection, tissue/graft rejection, and in the proliferation, survival, differentiation, or activation of a variety of hematopoietic cell lineages. Similarly, expression at elevated levels in the brain, and in other tissues, suggests that this protein may be involved in the proliferation, stimulation, or differentiation of other cell lineages as well, including neurons and mesenchymal cells. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:11 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2315 of SEQ ID NO:11, b is an integer of 15 to 2329, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:11, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 2
The translation product of this gene shares sequence homology with the PC-1 protein, that is a membrane glycoprotein that is selectively expressed on the surface of antibody-secreting cells. It also displays homology with alkaline phosphodiesterase I, and autotaxin, a tumor cell motility-stimulating protein. Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with membrane glycoprotein and/or autotaxin proteins. Such activities are known in the art, some of which are described elsewhere herein.
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 411-427 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 428 to 453 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ia membrane proteins.
This gene is expressed primarily in human ovarian tumors.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: reproductive diseases and/or disorders, particularly ovarian cancer and tumor cell metastasis. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the reproductive system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., reproductive, ovarian, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 83 as residues: Gly-17 to His-22, Lys-100 to Asp-109, Gln-124 to Ser-130, Glu-186 to Glu-201, Asp-237 to Lys-247, His-304 to Ile-311, Asp-335 to Leu-342, Ala-355 to Thr-364, Pro-382 to His-391, Gln-444 to Leu-451. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in ovarian cancer and homology to autotaxin indicates that polynucleotides and polypeptides corresponding to this gene are useful for the diagnosis and/or treatment of cancer. Autotaxin is a tumor cell motility-stimulating protein. The gene described herein in this patent application is only detected in ovarian tumors. Therefore, it may represent a key player in the diagnosis or treatment in particular of ovarian cancer, and possibly of cancers in general. It may particularly represent a target for inhibitors to control the spread of such cancers. Similarly, the expression within cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation. Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA). Alternatively, this gene product may be involved in the pattern of cellular proliferation that accompanies early embryogenesis. Thus, aberrant expression of this gene product in tissuesxe2x80x94particularly adult tissuesxe2x80x94may correlate with patterns of abnormal cellular proliferation, such as found in various cancers. Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus this protein may modulate apoptosis or tissue differentiation and would be useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:12 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2316 of SEQ ID NO:12, b is an integer of 15 to 2330, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:12, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 3
The translation product of this gene shares sequence homology with murine proline-rich acidic protein (Genbank Accession No: AAC24897).
This gene is expressed primarily in fetal liver and tumors of the liver (hepatoma) and to a lesser extent in normal and malignant colon as well as breast cancer.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: inflammatory diseases and/or cancers of the liver, colon or breast. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the gastrointestinal or hepatic system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., gastrointestinal, hepatic, metabolic, reproductive, endocrine, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, breast milk, chyme, bile, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 84 as residues: Trp-35 to Trp-46, Pro-53 to Asp-58, Thr-74 to Arg-83, Pro-106 to Leu-113, Pro-116 to Arg-128, Pro-141 to Gln-152. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in human colon tissue indicates that polynucleotides and polypeptides corresponding to this gene are useful for diagnosis and or treatment of tumors of the colon or liver or for inflammatory disorders of theses tissues such as inflammatory bowel disease. Moreover, the protein product of this clone is useful for the detection and treatment of liver disorders and cancers. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d, xe2x80x9cInfectious Diseasexe2x80x9d, and xe2x80x9cBinding Activityxe2x80x9d sections below, in Example 11, and 27, and elsewhere herein. Briefly, the protein can be used for the detection, treatment, and/or prevention of hepatoblastoma, jaundice, hepatitis, liver metabolic diseases and conditions that are attributable to the differentiation of hepatocyte progenitor cells. In addition the expression in fetus would suggest a useful role for the protein product in developmental abnormalities, fetal deficiencies, pre-natal disorders and various would-healing models and/or tissue trauma. The protein is useful for modulating the immune response to aberrant polypeptides, as may exist in rapidly proliferating cells and tissues (e.g., colon, breast, and liver cancer tissue). Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:13 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 637 of SEQ ID NO:13, b is an integer of 15 to 651, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:13, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 4
The translation product of this gene shares sequence homology with the human complement subcomponent C1q chain A precursor (see, e.g., GenBank accession AAD32626), which is thought to be important in immune responses.
It has been discovered that this gene is expressed primarily in immune and hemopoietic cells and to a lesser extent in various cancer cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: disorders of the immune and hemopoietic systems and cancer. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune and hemopoietic systems, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 85 as residues: Pro-29 to Gly-46, Lys-48 to Gly-55, Lys-67 to Gly-80, Lys-100 to Pro-115, Arg-121 to Gly-127, Asn-139 to Gly-149, Ser-179 to Arg-185, Asp-191 to Gly-196, Lys-219 to Gly-224. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution and homology to complement subcomponent C1q chain A precursor suggests that the protein product of this clone would be useful for treatment and diagnosis of diseases of the immune and hemopoietic systems and cancers. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma.
Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:14 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 983 of SEQ ID NO:14, b is an integer of 15 to 997, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:14, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 5
The translation product of this gene shares sequence homology with, and is believed to be a novel homolog of, the human complement C1r protein (gb|AAA51851.1|human complement C1r [Homo sapiens]) an inactive precursor of a serine protease which is thought to be important in activation of the complement pathway in human immunity (See, for example, Biochemistry 25 (17), 4855-4863 (1986); all information within this reference is hereby incorporated herein by reference). The homologous regions are shown below:
Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with serine protease zymogens such as C1r. Such activities are known in the art, some of which are described elsewhere herein.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of the following amino acid sequence:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in kidney (e.g., fetal kidney, rejected Kidney transplant, and cancerous kidney tissue) Human OB MG63 control fraction I (osteosarcoma); Human Adult Testes, Large Inserts, Reexcision; and Rejected Kidney, lib 4.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: reproductive, and renal diseases and/or disorders, including immune suppression and other diseases of the immune system. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., immune, renal, reproductive, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, seminal fluid, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 86 as residues: Pro-32 to Lys-49, Glu-66 to Ala-72, Asp-84 to Gly-90, Arg-117 to Thr-126, Pro-161 to Tyr-176, Gly-191 to Glu-201, Leu-270 to Ser-275, Pro-303 to Ser-314, Asp-339 to Tyr-344, Gln-384 to Lys-396. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The homology of the translation product of this gene to the human C1r indicates that polynucleotides and polypeptides corresponding to this gene are useful for diagnosis and treatment of diseases of the immune system including AIDS and other immune deficiencies, autoimmune disorders such as lupus, and other immune disorders. Alternatively, the distribution in testicular tissue indicates that polynucleotides and polypeptides corresponding to this gene are useful for the treatment and diagnosis of conditions concerning proper testicular function (e.g. endocrine function, sperm maturation), as well as cancer. Therefore, this gene product is useful in the treatment of male infertility and/or impotence. This gene product is also useful in assays designed to identify binding agents, as such agents (antagonists) are useful as male contraceptive agents. Similarly, the protein is believed to be useful in the treatment and/or diagnosis of testicular cancer. The testes are also a site of active gene expression of transcripts that is expressed, particularly at low levels, in other tissues of the body. Therefore, this gene product may be expressed in other specific tissues or organs where it may play related functional roles in other processes, such as hematopoiesis, inflammation, bone formation, and kidney function, to name a few possible target indications. Alternatively, the tissue distribution in kidney indicates that the protein product of this clone could be used in the treatment and/or detection of kidney diseases including renal failure, nephritis, renal tubular acidosis, proteinuria, pyuria, edema, pyelonephritis, hydronephritis, nephrotic syndrome, crush syndrome, glomerulonephritis, hematuria, renal colic and kidney stones, in addition to Wilm""s Tumor Disease, and congenital kidney abnormalities such as horseshoe kidney, polycystic kidney, and Falconi""s syndrome. The protein is useful in modulating the immune response to aberrant polypeptides (as may exist in rapidly proliferating cells and tissues), and presents a novel therapeutic for hemophiliacs and other patients presenting aberrant blood diseases and/or disorders. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:15 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1252 of SEQ ID NO:15, b is an integer of 15 to 1266, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:15, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 6
The translation product of this gene shares sequence homology with Bos taurus mimecan (see GenBank accession AAB70264), which is though to be important in connective tissues. Based on this homology it is expected that these proteins will share some biological activity.
It has been discovered that this gene is expressed primarily in fetal tissues, aorta, cochlea and to a lesser extent in a variety of other tissues and cell types.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: heart disease, restenosis, atherosclerosis, stoke, angina, thrombosis, and wound healing, deafness and vertigo. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the connective tissue, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., immune, nervous, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 87 as residues: Pro-21 to Arg-28, Tyr-33 to Phe-38, Gln-45 to Glu-61, Pro-83 to Glu-90, Lys-195 to Ile-204, Thr-253 to Tyr-262. Polynucleotides encoding said polypeptides are also encompassed by the invention.
Mimecan is a member of a group of small, leucine-rich proteoglycans (SLRPs). These proteins share a common core structure which consists of a central domain with varying numbers of leucine-rich repeats flanked by cysteine-rich clusters. Seven members of SLRPs have been described so far. These include: keratocan, lumican, fibromodulin, decorin, biglycan, and epiphycan. A seventh member of the family, mimecan, is a proteoglycan expressed by many connective tissues. It was originally isolated in a truncated form as a bone-associated glycoprotein, osteoglycin. Mimecan has since been demonstrated to be expressed in a variety of tissues, with and without keratan sulfate chains. Numerous examples illustrate the ability of SLRPs to bind growth factors and/or growth factor receptors and therefore to modulate cell proliferation and differentiation.
The tissue distribution and homology to mimecan suggests that the protein product of this clone would be useful for the treatment and diagnosis of conditions involving tissue repair and wound healing. Tissue repair may be indicated in cases of injury to the skin or internal organs, ulceration, cellular necrosis or other conditions involving healing of both diseased or non-diseased, traumatized tissue.
More specifically, the expression in aorta would suggest a role in cardiovascular disorders such as, asthma, heart disease, restenosis, atherosclerosis, stoke, angina and thrombosis. The expression in cochlea would suggest a potential use in the treatment of conditions affecting the inner ear, such as deafness and vertigo. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. In addition, because of the implications of tissue regeneration, remodeling and growth regulation, and in light of the high degree of expression in fetal and cancerous tissues, the protein product of this gene may have indications in the diagnosis and treatment of neoplasms and cancer. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:16 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2696 of SEQ ID NO:16, b is an integer of 15 to 2710, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:16, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 7
The translation product of this gene shares sequence homology with the rat decay accelerating factor (see, e.g., GenBank accession AAC77439) which is thought to be important in modifying the activity and cellular response of complement proteins and thus attenuating complement mediated immune responses.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of this polypeptide (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridize, under stringent conditions, to the polynucleotide encoding this polypeptide are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding this polypeptide are also encompassed by the invention.
In specific embodiments, polynucleotides of the invention comprise, or alternatively consists of, the following polynucleotide sequence:
Moreover, fragments and variants of this polynucleotide (such as, for example, fragments as described herein, polynucleotides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to this polynucleotide and polynucleotides which hybridize, under stringent conditions, to this polynucleotide are encompassed by the invention. Polypeptides encoded by these polynucleotides are also encompassed by the invention as are antibodies which bind to such polypeptides.
It has been discovered that this gene is expressed primarily in ovarian tumor.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: reproductive diseases and/or disorders, particularly ovarian tumors. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the reproductive system, expression of this gene at significantly higher or lower levels may be detected in certain tissues or cell types (e.g., reproductive, ovarian, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
The tissue distribution in ovarian tumor tissue indicates that polynucleotides and polypeptides of the invention are useful for the detection, treatment, and/or prevention of proliferative diseases and/or disorders, and particularly for ovarian cancer. Moreover, the expression within cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation. Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA). Alternatively, this gene product may be involved in the pattern of cellular proliferation that accompanies early embryogenesis. Thus, aberrant expression of this gene product in tissuesxe2x80x94particularly adult tissuesxe2x80x94may correlate with patterns of abnormal cellular proliferation, such as found in various cancers. Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus this protein may modulate apoptosis or tissue differentiation and would be useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation.
Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:17 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2391 of SEQ ID NO:17, b is an integer of 15 to 2405, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:17, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 8
Angiogenesis, the formation of new blood vessels from pre-existing vasculature, is a tightly regulated process in normal adults. Under physiological circumstances, growth of new capillaries is tightly controlled by an interplay of growth regulatory proteins which act either to stimulate or to inhibit blood vessel growth. Normally, the balance between these forces is tipped in favor of inhibition and consequently blood vessel growth is restrained. Under certain pathological circumstances, however, local inhibitory controls are unable to restrain the increased activity of angiogenic inducers. Angiogenesis is a key step in the metastasis of cancer (Folkman, Nature Med. 1:27-31 (1995)) and in abnormal wound healing, inflammation, rheumatoid arthritis, psoriasis, and diabetic retinopathy, it is integral to the pathology (Folkman et al., Science 235:442-447 (1987)), engendering the hope that these pathological entities could be regulated by pharmacological and/or genetic suppression of blood vessel growth (Iruela-Arispe et al., Thromb. Haem. 78:672-677 1997)).
Thrombospondin-1 (TSP-1) is a 450 kDa, anti-angiogenic adhesive glycoprotein released from activated platelets and secreted by growing cells (reviewed in Adams, Int. J. Biochem. Cell Biol. 29:861-865 (1997)). TSP-1 is a homotrimer, with each subunit comprised of a 1152 amino acid residue polypeptide, post-translationally modified by N-linked glycosylation and beta-hydroxylation of asparagine residues.
TSP-1 protein and mRNA levels are regulated by a variety of factors. TSP-1 protein levels are down-regulated by IL-1 alpha and TNF alpha. TSP-1 mRNA and protein levels are up-regulated by polypeptide growth factors including PDGF, TGF-beta, and bFGF (Bornstein, FASEB J. 6:3290-3299 (1992)) and are also regulated by the level of expression of the p53 tumor suppressor gene product (Dameron et al., Science 265:1582-1584 (1994)). At least four other members of the thrombospondin family have been identified: TSP-2, TSP-3, TSP-4, and TSP-5 (also called COMP). There is a need in the art to identify other molecules involved in the regulation of angiogenesis.
FIGS. 4A-4H shows the nucleotide sequence (SEQ ID NO:18) and the deduced amino acid sequence (SEQ ID NO:89) of THRAP. The predicted leader sequence located at about amino acid residues 1 to 28 is bolded in FIGS. 4A-4H. FIGS. 4A-4H also shows 13 TSP-1-like domains (indicated by single underlined amino acid residues), an IgG-like domain (indicated by bolded and double underlined amino acid residues), and a proteinase inhibitor-like domain (indicated by double underlined amino acid residues) of SEQ ID NO:89. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes.
FIGS. 5A-5E shows the regions of identity between the amino acid sequence of THRAP and the translation product of Thrombospondin-like protein
determined by BLAST analysis. Identical amino acids between the two polypeptides are boxed. By examining the regions of boxed amino acids, the skilled artisan can readily identify conserved domains between the two polypeptides. These conserved domains are preferred embodiments of the present invention.
FIG. 6 shows an analysis of the THRAP amino acid sequence. Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity; amphipathic regions; flexible regions; antigenic index and surface probability are shown, and all were generated using the default settings. In the xe2x80x9cAntigenic Index or Jameson-Wolfxe2x80x9d graph, the positive peaks indicate locations of the highly antigenic regions of the THRAP protein, i.e., regions from which epitope-bearing peptides of the invention can be obtained. The domains defined by these graphs are contemplated by the present invention.
The data presented in FIG. 6 are also represented in tabular form in Table 7. The columns are labeled with the headings xe2x80x9cResxe2x80x9d, xe2x80x9cPositionxe2x80x9d, and Roman Numerals I-XIV. The column headings refer to the following features of the amino acid sequence presented in FIG. 6, and Table 7: xe2x80x9cResxe2x80x9d: amino acid residue of SEQ ID NO:89 and FIGS. 4A-4H; xe2x80x9cPositionxe2x80x9d: position of the corresponding residue within SEQ ID NO:89 and FIGS. 4A-4H; I: Alpha, Regionsxe2x80x94Garnier-Robson; II: Alpha, Regionsxe2x80x94Chou-Fasman; III: Beta, Regionsxe2x80x94Garnier-Robson; IV: Beta, Regionsxe2x80x94Chou-Fasman; V: Turn, Regionsxe2x80x94Garnier-Robson; VI: Turn, Regionsxe2x80x94Chou-Fasman; VII: Coil, Regionsxe2x80x94Garnier-Robson; VIII: Hydrophilicity Plotxe2x80x94Kyte-Doolittle; IX: Hydrophobicity Plotxe2x80x94Hopp-Woods; X: Alpha, Amphipathic Regionsxe2x80x94Eisenberg; XI: Beta, Amphipathic Regionsxe2x80x94Eisenberg; XII: Flexible Regionsxe2x80x94Karplus-Schulz; XIII: Antigenic Indexxe2x80x94Jameson-Wolf; and XIV: Surface Probability Plotxe2x80x94Emini.
A clone (HOHCA60) containing all or most of the sequence for SEQ ID NO:18 was deposited with the American Type Culture Collection (xe2x80x9cATCC(copyright)xe2x80x9d) on Sep. 7, 1999, and was given the ATCC Deposit Number PTA-627. The ATCC is located at 10801 University Boulevard, Manassas, Va. 20110-2209, USA. The ATCC deposit was made pursuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for purposes of patent procedure. Clone HOHCA60 was isolated from a osteoblast II cDNA library. This clone contains the entire coding region identified as SEQ ID NO:18. The deposited clone contains a cDNA having a total of 5720 nucleotides, which encodes a predicted open reading frame of 1745 amino acid residues. (See FIGS. 4A-4H.) The open reading frame begins at a N-terminal methionine located at nucleotide position 67, and ends at a stop codon at nucleotide position 5302. The predicted molecular weight of the THRAP protein is about 191 kDa.
Subsequent Northern analysis also showed that this gene is expressed primarily in testes, fetal tissue (e.g., lung, heart), synovial sarcoma, brain, immune cells and tissues (e.g., lymph node, macrophage), colon, prostate, small intestine, thyroid and to a lesser extent in many other tissues.
DOMAINS: It has also been discovered that THRAP (SEQ ID NO:89) contains 13 TSP-1-like domains, an IgG-like domain, and a proteinase inhibitor-like domain. More particularly, (a) a predicted TSP-1-like domain1 (SEQ ID NO:161) located at about amino acids 33 to 82 of SEQ ID NO:89; (b) a predicted TSP-1-like domain2 (SEQ ID NO:162) located at about amino acids 301-360 of SEQ ID NO:89; (c) a predicted TSP-1-like domain3 (SEQ ID NO:163) located at about amino acids 363-421 of SEQ ID NO:89, (d) a predicted TSP-1-like domain4 (SEQ ID NO:164) located at about amino acids 423-475 of SEQ ID NO:89, (e) a predicted TSP-1-like domain5 (SEQ ID NO:165) located at about amino acids 514-566 of SEQ ID NO:89, (f) a predicted TSP-1-like domain6 (SEQ ID NO:166) located at about amino acids 590-650 of SEQ ID NO:89, (g) a predicted TSP-1-like domain7 (SEQ ID NO:167) located at about amino acids 653-712 SEQ ID NO:89, (h) a predicted TSP-1-like domain8 (SEQ ID NO:168) located at about amino acids 715-772 of SEQ ID NO:89, (i) a predicted TSP-1-like domain9 (SEQ ID NO:169) located at about amino acids 775-832 of SEQ ID NO:89, (j) a predicted TSP-1-like domain10 (SEQ ID NO: 170) located at about amino acids 1473-1529 SEQ ID NO:89, (k) a predicted TSP-1-like domain11 (SEQ ID NO:171) located at about amino acids 1532-1590 of SEQ ID NO:89, (l) a predicted TSP-1-like domain12 (SEQ ID NO:172) located at about amino acids 1593-1650 of SEQ ID NO:89, (m) a predicted TSP-1-like domain13 (SEQ ID NO:173) located at about amino acids 1653-1708 SEQ ID NO:89, (n) a predicted proteinase inhibitor domain (SEQ ID NO:174) located at about amino acids 83-220 of SEQ ID NO:89, and (o) a predicted IgG-like domain (SEQ ID NO:175) located at about amino acids 1180-1471 of SEQ ID NO:89. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes. These polypeptide fragments of THRAP are specifically contemplated in the present invention.
SIGNAL SEQUENCE. Moreover, the encoded polypeptide has a THRAP leader sequence located at about amino acids 1-28. (See FIGS. 4A-4H.) Also shown in FIGS. 4A-4H, the THRAP secreted protein encompasses about amino acid residues 29-1745. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes. These polypeptide fragments of THRAP are specifically contemplated in the present invention.
N-terminal deletions of the THRAP polypeptide can be described by the general formula m-1745, where m is an integer from 2 to 1739 where m corresponds to the position of the amino acid residue identified in SEQ ID NO:89. More in particular, the invention provides polynucleotides encoding polypeptides comprising, or alternatively consisting of, an amino acid sequence selected from the group: E-2 to A-1745; C-3 to A-1745; C-4 to A-1745; R-5 to A-1745; R-6 to A-1745; A-7 to A-1745; T-8 to A-1745; P-9 to A-1745; G-10 to A-1745; T-11 to A-1745; L-12 to A-1745; L-13 to A-1745; L-14 to A-1745; F-15 to A-1745; L-16 to A-1745; A-17 to A-1745; F-18 to A-1745; L-19 to A-1745; L-20 to A-1745; L-21 to A-1745; S-22 to A-1745; S-23 to A-1745; R-24 to A-1745; T-25 to A-1745; A-26 to A-1745; R-27 to A-1745; S-28 to A-1745; E-29 to A-1745; E-30 to A-1745; D-31 to A-1745; R-32 to A-1745; D-33 to A-1745; G-34 to A-1745; L-35 to A-1745; W-36 to A-1745; D-37 to A-1745; A-38 to A-1745; W-39 to A-1745; G-40 to A-1745; P-41 to A-1745; W-42 to A-1745; S-43 to A-1745; E-44 to A-1745; C-45 to A-1745; S-46 to A-1745; R-47 to A-1745; T-48 to A-1745; C-49 to A-1745; G-50 to A-1745; G-51 to A-1745; G-52 to A-1745; A-53 to A-1745; S-54 to A-1745; Y-55 to A-1745; S-56 to A-1745; L-57 to A-1745; R-58 to A-1745; R-59 to A-1745; C-60 to A-1745; L-61 to A-1745; S-62 to A-1745; S-63 to A-1745; K-64 to A-1745; S-65 to A-1745; C-66 to A-1745; E-67 to A-1745; G-68 to A-1745; R-69 to A-1745; N-70 to A-1745; I-71 to A-1745; R-72 to A-1745; Y-73 to A-1745; R-74 to A-1745; T-75 to A-1745; C-76 to A-1745; S-77 to A-1745; N-78 to A-1745; V-79 to A-1745; D-80 to A-1745; C-81 to A-1745; P-82 to A-1745; P-83 to A-1745; E-84 to A-1745; A-85 to A-1745; G-86 to A-1745; D-87 to A-1745; F-88 to A-1745; R-89 to A-1745; A-90 to A-1745; Q-91 to A-1745; Q-92 to A-1745; C-93 to A-1745; S-94 to A-1745; A-95 to A-1745; H-96 to A-1745; N-97 to A-1745; D-98 to A-1745; V-99 to A-1745; K-100 to A-1745; H-101 to A-1745; H-102 to A-1745; G-103 to A-1745; Q-104 to A-1745; F-105 to A-1745; Y-106 to A-1745; E-107 to A-1745; W-108 to A-1745; L-109 to A-1745; P-110 to A-1745; V-111 to A-1745; S-112 to A-1745; N-113 to A-1745; D-114 to A-1745; P-115 to A-1745; D-116 to A-1745; N-117 to A-1745; P-118 to A-1745; C-119 to A-1745; S-120 to A-1745; L-121 to A-1745; K-122 to A-1745; C-123 to A-1745; Q-124 to A-1745; A-125 to A-1745; K-126 to A-1745; G-127 to A-1745; T-128 to A-1745; T-129 to A-1745; L-130 to A-1745; V-131 to A-1745; V-132 to A-1745; E-133 to A-1745; L-134 to A-1745; A-135 to A-1745; P-136 to A-1745; K-137 to A-1745; V-138 to A-1745; L-139 to A-1745; D-140 to A-1745; G-141 to A-1745; T-142 to A-1745; R-143 to A-1745; C-144 to A-1745; Y-145 to A-1745; T-146 to A-1745; E-147 to A-1745; S-148 to A-1745; L-149 to A-1745; D-150 to A-1745; M-151 to A-1745; C-152 to A-1745; I-153 to A-1745; S-154 to A-1745; G-155 to A-1745; L-156 to A-1745; C-157 to A-1745; Q-158 to A-1745; I-159 to A-1745; V-160 to A-1745; G-161 to A-1745; C-162 to A-1745; D-163 to A-1745; H-164 to A-1745; Q-165 to A-1745; L-166 to A-1745; G-167 to A-1745; S-168 to A-1745; T-169 to A-1745; V-170 to A-1745; K-171 to A-1745; E-172 to A-1745; D-173 to A-1745; N-174 to A-1745; C-175 to A-1745; G-176 to A-1745; V-177 to A-1745; C-178 to A-1745; N-179 to A-1745; G-180 to A-1745; D-181 to A-1745; G-182 to A-1745; S-183 to A-1745; T-184 to A-1745; C-185 to A-1745; R-186 to A-1745; L-187 to A-1745; V-188 to A-1745; R-189 to A-1745; G-190 to A-1745; Q-191 to A-1745; Y-192 to A-1745; K-193 to A-1745; S-194 to A-1745; Q-195 to A-1745; L-196 to A-1745; S-197 to A-1745; A-198 to A-1745; T-199 to A-1745; K-200 to A-1745; S-201 to A-1745; D-202 to A-1745; D-203 to A-1745; T-204 to A-1745; V-205 to A-1745; V-206 to A-1745; A-207 to A-1745; I-208 to A-1745; P-209 to A-1745; Y-210 to A-1745; G-211 to A-1745; S-212 to A-1745; R-213 to A-1745; H-214 to A-1745; I-215 to A-1745; R-216 to A-1745; L-217 to A-1745; V-218 to A-1745; L-219 to A-1745; K-220 to A-1745; G-221 to A-1745; P-222 to A-1745; D-223 to A-1745; H-224 to A-1745; L-225 to A-1745; Y-226 to A-1745; L-227 to A-1745; E-228 to A-1745; T-229 to A-1745; K-230 to A-1745; T-231 to A-1745; L-232 to A-1745; Q-233 to A-1745; G-234 to A-1745; T-235 to A-1745; K-236 to A-1745; G-237 to A-1745; E-238 to A-1745; N-239 to A-1745; S-240 to A-1745; L-241 to A-1745; S-242 to A-1745; S-243 to A-1745; T-244 to A-1745; G-245 to A-1745; T-246 to A-1745; F-247 to A-1745; L-248 to A-1745; V-249 to A-1745; D-250 to A-1745; N-251 to A-1745; S-252 to A-1745; S-253 to A-1745; V-254 to A-1745; D-255 to A-1745; F-256 to A-1745; Q-257 to A-1745; K-258 to A-1745; F-259 to A-1745; P-260 to A-1745; D-261 to A-1745; K-262 to A-1745; E-263 to A-1745; I-264 to A-1745; L-265 to A-1745; R-266 to A-1745; M-267 to A-1745; A-268 to A-1745; G-269 to A-1745; P-270 to A-1745; L-271 to A-1745; T-272 to A-1745; A-273 to A-1745; D-274 to A-1745; F-275 to A-1745; I-276 to A-1745; V-277 to A-1745; K-278 to A-1745; I-279 to A-1745; R-280 to A-1745; N-281 to A-1745; S-282 to A-1745; G-283 to A-1745; S-284 to A-1745; A-285 to A-1745; D-286 to A-1745; S-287 to A-1745; T-288 to A-1745; V-289 to A-1745; Q-290 to A-1745; F-291 to A-1745; I-292 to A-1745; F-293 to A-1745; Y-294 to A-1745; Q-295 to A-1745; P-296 to A-1745; I-297 to A-1745; I-298 to A-1745; H-299 to A-1745; R-300 to A-1745; W-301 to A-1745; R-302 to A-1745; E-303 to A-1745; T-304 to A-1745; D-305 to A-1745; F-306 to A-1745; F-307 to A-1745; P-308 to A-1745; C-309 to A-1745; S-310 to A-1745; A-311 to A-1745; T-312 to A-1745; C-313 to A-1745; G-314 to A-1745; G-315 to A-1745; G-316 to A-1745; Y-317 to A-1745; Q-318 to A-1745; L-319 to A-1745; T-320 to A-1745; S-321 to A-1745; A-322 to A-1745; E-323 to A-1745; C-324 to A-1745; Y-325 to A-1745; D-326 to A-1745; L-327 to A-1745; R-328 to A-1745; S-329 to A-1745; N-330 to A-1745; R-331 to A-1745; V-332 to A-1745; V-333 to A-1745; A-334 to A-1745; D-335 to A-1745; Q-336 to A-1745; Y-337 to A-1745; C-338 to A-1745; H-339 to A-1745; Y-340 to A-1745; Y-341 to A-1745; P-342 to A-1745; E-343 to A-1745; N-344 to A-1745; I-345 to A-1745; K-346 to A-1745; P-347 to A-1745; K-348 to A-1745; P-349 to A-1745; K-350 to A-1745; L-351 to A-1745; Q-352 to A-1745; E-353 to A-1745; C-354 to A-1745; N-355 to A-1745; L-356 to A-1745; D-357 to A-1745; P-358 to A-1745; C-359 to A-1745; P-360 to A-1745; A-361 to A-1745; R-362 to A-1745; W-363 to A-1745; E-364 to A-1745; A-365 to A-1745; T-366 to A-1745; P-367 to A-1745; W-368 to A-1745; T-369 to A-1745; A-370 to A-1745; C-371 to A-1745; S-372 to A-1745; S-373 to A-1745; S-374 to A-1745; C-375 to A-1745; G-376 to A-1745; G-377 to A-1745; G-378 to A-1745; I-379 to A-1745; Q-380 to A-1745; S-381 to A-1745; R-382 to A-1745; A-383 to A-1745; V-384 to A-1745; S-385 to A-1745; C-386 to A-1745; V-387 to A-1745; E-388 to A-1745; E-389 to A-1745; D-390 to A-1745; W-396 to A-1745; Q-392 to A-1745; G-393 to A-1745; H-394 to A-1745; V-395 to A-1745; T-396 to A-1745; S-397 to A-1745; V-398 to A-1745; E-399 to A-1745; E-400 to A-1745; W-401 to A-1745; K-402 to A-1745; C-403 to A-1745; M-404 to A-1745; Y-405 to A-1745; T-406 to A-1745; P-407 to A-1745; K-408 to A-1745; M-409 to A-1745; P-410 to A-1745; I-411 to A-1745; A-412 to A-1745; Q-413 to A-1745; P-414 to A-1745; C-415 to A-1745; N-416 to A-1745; I-417 to A-1745; F-418 to A-1745; D-419 to A-1745; C-420 to A-1745; P-421 to A-1745; K-422 to A-1745; W-423 to A-1745; L-424 to A-1745; A-425 to A-1745; Q-426 to A-1745; Q-427 to A-1745; W-428 to A-1745; S-429 to A-1745; P-430 to A-1745; C-431 to A-1745; T-432 to A-1745; V-433 to A-1745; T-434 to A-1745; C-435 to A-1745; G-436 to A-1745; Q-437 to A-1745; G-438 to A-1745; L-439 to A-1745; R-440 to A-1745; Y-441 to A-1745; R-442 to A-1745; V-443 to A-1745; V-444 to A-1745; L-445 to A-1745; C-446 to A-1745; I-447 to A-1745; D-448 to A-1745; H-449 to A-1745; R-450 to A-1745; G-451 to A-1745; M-452 to A-1745; H-453 to A-1745; T-454 to A-1745; G-455 to A-1745; G-456 to A-1745; C-457 to A-1745; S-458 to A-1745; P-459 to A-1745; K-460 to A-1745; T-461 to A-1745; K-462 to A-1745; P-463 to A-1745; H-464 to A-1745; I-465 to A-1745; K-466 to A-1745; E-467 to A-1745; E-468 to A-1745; C-469 to A-1745; I-470 to A-1745; V-471 to A-1745; P-472 to A-1745; T-473 to A-1745; P-474 to A-1745; C-475 to A-1745; Y-476 to A-1745; K-477 to A-1745; P-478 to A-1745; K-479 to A-1745; E-480 to A-1745; K-481 to A-1745; L-482 to A-1745; P-483 to A-1745; V-484 to A-1745; E-485 to A-1745; A-486 to A-1745; K-487 to A-1745; L-488 to A-1745; P-489 to A-1745; W-490 to A-1745; F-491 to A-1745; K-492 to A-1745; Q-493 to A-1745; A-494 to A-1745; Q-495 to A-1745; E-496 to A-1745; L-497 to A-1745; E-498 to A-1745; E-499 to A-1745; G-500 to A-1745; A-501 to A-1745; A-502 to A-1745; V-503 to A-1745; S-504 to A-1745; E-505 to A-1745; E-506 to A-1745; P-507 to A-1745; S-508 to A-1745; F-509 to A-1745; I-510 to A-1745; P-511 to A-1745; K-512 to A-1745; A-513 to A-1745; W-514 to A-1745; S-515 to A-1745; A-516 to A-1745; C-517 to A-1745; T-518 to A-1745; V-519 to A-1745; T-520 to A-1745; C-521 to A-1745; G-522 to A-1745; V-523 to A-1745; G-524 to A-1745; T-525 to A-1745; Q-526 to A-1745; V-527 to A-1745; R-528 to A-1745; I-529 to A-1745; V-530 to A-1745; R-531 to A-1745; C-532 to A-1745; Q-533 to A-1745; V-534 to A-1745; L-535 to A-1745; L-536 to A-1745; S-537 to A-1745; F-538 to A-1745; S-539 to A-1745; Q-540 to A-1745; S-541 to A-1745; V-542 to A-1745; A-543 to A-1745; D-544 to A-1745; L-545 to A-1745; P-546 to A-1745; I-547 to A-1745; D-548 to A-1745; E-549 to A-1745; C-550 to A-1745; E-551 to A-1745; G-552 to A-1745; P-553 to A-1745; K-554 to A-1745; P-555 to A-1745; A-556 to A-1745; S-557 to A-1745; Q-558 to A-1745; R-559 to A-1745; A-560 to A-1745; C-561 to A-1745; Y-562 to A-1745; A-563 to A-1745; G-564 to A-1745; P-565 to A-1745; C-566 to A-1745; S-567 to A-1745; G-568 to A-1745; E-569 to A-1745; I-570 to A-1745; P-571 to A-1745; E-572 to A-1745; F-573 to A-1745; N-574 to A-1745; P-575 to A-1745; D-576 to A-1745; E-577 to A-1745; T-578 to A-1745; D-579 to A-1745; G-580 to A-1745; L-581 to A-1745; F-582 to A-1745; G-583 to A-1745; G-584 to A-1745; L-585 to A-1745; Q-586 to A-1745; D-587 to A-1745; F-588 to A-1745; D-589 to A-1745; E-590 to A-1745; L-591 to A-1745; Y-592 to A-1745; D-593 to A-1745; W-594 to A-1745; E-595 to A-1745; Y-596 to A-1745; E-597 to A-1745; G-598 to A-1745; F-599 to A-1745; T-600 to A-1745; K-601 to A-1745; C-602 to A-1745; S-603 to A-1745; E-604 to A-1745; S-605 to A-1745; C-606 to A-1745; G-607 to A-1745; G-608 to A-1745; G-609 to A-1745; V-610 to A-1745; Q-611 to A-1745; E-612 to A-1745; A-613 to A-1745; V-614 to A-1745; V-615 to A-1745; S-616 to A-1745; C-617 to A-1745; L-618 to A-1745; N-619 to A-1745; K-620 to A-1745; Q-621 to A-1745; T-622 to A-1745; R-623 to A-1745; E-624 to A-1745; P-625 to A-1745; A-626 to A-1745; E-627 to A-1745; E-628 to A-1745; N-629 to A-1745; L-630 to A-1745; C-631 to A-1745; V-632 to A-1745; T-633 to A-1745; S-634 to A-1745; R-635 to A-1745; R-636 to A-1745; P-637 to A-1745; P-638 to A-1745; Q-639 to A-1745; L-640 to A-1745; L-641 to A-1745; K-642 to A-1745; S-643 to A-1745; C-644 to A-1745; N-645 to A-1745; L-646 to A-1745; D-647 to A-1745; P-648 to A-1745; C-649 to A-1745; P-650 to A-1745; A-651 to A-1745; R-652 to A-1745; W-653 to A-1745; E-654 to A-1745; I-655 to A-1745; G-656 to A-1745; K-657 to A-1745; W-658 to A-1745; S-659 to A-1745; P-660 to A-1745; C-661 to A-1745; S-662 to A-1745; L-663 to A-1745; T-664 to A-1745; C-665 to A-1745; G-666 to A-1745; V-667 to A-1745; G-668 to A-1745; L-669 to A-1745; Q-670 to A-1745; T-671 to A-1745; R-672 to A-1745; D-673 to A-1745; V-674 to A-1745; F-675 to A-1745; C-676 to A-1745; S-677 to A-1745; H-678 to A-1745; L-679 to A-1745; L-680 to A-1745; S-681 to A-1745; R-682 to A-1745; E-683 to A-1745; M-684 to A-1745; N-685 to A-1745; E-686 to A-1745; T-687 to A-1745; V-688 to A-1745; I-689 to A-1745; L-690 to A-1745; A-691 to A-1745; D-692 to A-1745; E-693 to A-1745; L-694 to A-1745; C-695 to A-1745; R-696 to A-1745; Q-697 to A-1745; P-698 to A-1745; K-699 to A-1745; P-700 to A-1745; S-701 to A-1745; T-702 to A-1745; V-703 to A-1745; Q-704 to A-1745; A-705 to A-1745; C-706 to A-1745; N-707 to A-1745; R-708 to A-1745; F-709 to A-1745; N-710 to A-1745; C-711 to A-1745; P-712 to A-1745; P-713 to A-1745; A-714 to A-1745; W-715 to A-1745; Y-716 to A-1745; P-717 to A-1745; A-718 to A-1745; Q-719 to A-1745; W-720 to A-1745; Q-721 to A-1745; P-722 to A-1745; C-723 to A-1745; S-724 to A-1745; R-725 to A-1745; T-726 to A-1745; C-727 to A-1745; G-728 to A-1745; G-729 to A-1745; G-730 to A-1745; V-731 to A-1745; Q-732 to A-1745; K-733 to A-1745; R-734 to A-1745; E-735 to A-1745; V-736 to A-1745; L-737 to A-1745; C-738 to A-1745; K-739 to A-1745; Q-740 to A-1745; R-741 to A-1745; M-742 to A-1745; A-743 to A-1745; D-744 to A-1745; G-745 to A-1745; S-746 to A-1745; F-747 to A-1745; L-748 to A-1745; E-749 to A-1745; L-750 to A-1745; P-751 to A-1745; E-752 to A-1745; T-753 to A-1745; F-754 to A-1745; C-755 to A-1745; S-756 to A-1745; A-757 to A-1745; S-758 to A-1745; K-759 to A-1745; P-760 to A-1745; A-761 to A-1745; C-762 to A-1745; Q-763 to A-1745; Q-764 to A-1745; A-765 to A-1745; C-766 to A-1745; K-767 to A-1745; K-768 to A-1745; D-769 to A-1745; D-770 to A-1745; C-771 to A-1745; P-772 to A-1745; S-773 to A-1745; E-774 to A-1745; W-775 to A-1745; L-776 to A-1745; L-777 to A-1745; S-778 to A-1745; D-779 to A-1745; W-780 to A-1745; T-781 to A-1745; E-782 to A-1745; C-783 to A-1745; S-784 to A-1745; T-785 to A-1745; S-786 to A-1745; C-787 to A-1745; G-788 to A-1745; E-789 to A-1745; G-790 to A-1745; T-791 to A-1745; Q-792 to A-1745; T-793 to A-1745; R-794 to A-1745; S-795 to A-1745; A-796 to A-1745; I-797 to A-1745; C-798 to A-1745; R-799 to A-1745; K-800 to A-1745; M-801 to A-1745; L-802 to A-1745; K-803 to A-1745; T-804 to A-1745; G-805 to A-1745; L-806 to A-1745; S-807 to A-1745; T-808 to A-1745; V-809 to A-1745; V-810 to A-1745; N-811 to A-1745; S-812 to A-1745; T-813 to A-1745; L-814 to A-1745; C-815 to A-1745; P-816 to A-1745; P-817 to A-1745; L-818 to A-1745; P-819 to A-1745; F-820 to A-1745; S-821 to A-1745; S-822 to A-1745; S-823 to A-1745; I-824 to A-1745; R-825 to A-1745; P-826 to A-1745; C-827 to A-1745; M-828 to A-1745; L-829 to A-1745; A-830 to A-1745; T-831 to A-1745; C-832 to A-1745; A-833 to A-1745; R-834 to A-1745; P-835 to A-1745; G-836 to A-1745; R-837 to A-1745; P-838 to A-1745; S-839 to A-1745; T-840 to A-1745; K-841 to A-1745; H-842 to A-1745; S-843 to A-1745; P-844 to A-1745; H-845 to A-1745; I-846 to A-1745; A-847 to A-1745; A-848 to A-1745; A-849 to A-1745; R-850 to A-1745; K-851 to A-1745; V-852 to A-1745; Y-853 to A-1745; I-854 to A-1745; Q-855 to A-1745; T-856 to A-1745; R-857 to A-1745; R-858 to A-1745; Q-859 to A-1745; R-860 to A-1745; K-861 to A-1745; L-862 to A-1745; H-863 to A-1745; F-864 to A-1745; V-865 to A-1745; V-866 to A-1745; G-867 to A-1745; G-868 to A-1745; F-869 to A-1745; A-870 to A-1745; Y-871 to A-1745; L-872 to A-1745; L-873 to A-1745; P-874 to A-1745; K-875 to A-1745; T-876 to A-1745; A-877 to A-1745; V-878 to A-1745; V-879 to A-1745; L-880 to A-1745; R-881 to A-1745; C-882 to A-1745; P-883 to A-1745; A-884 to A-1745; R-885 to A-1745; R-886 to A-1745; V-887 to A-1745; R-888 to A-1745; K-889 to A-1745; P-890 to A-1745; L-891 to A-1745; I-892 to A-1745; T-893 to A-1745; W-894 to A-1745; E-895 to A-1745; K-896 to A-1745; D-897 to A-1745; G-898 to A-1745; Q-899 to A-1745; H-900 to A-1745; L-901 to A-1745; I-902 to A-1745; S-903 to A-1745; S-904 to A-1745; T-905 to A-1745; H-906 to A-1745; V-907 to A-1745; T-908 to A-1745; V-909 to A-1745; A-910 to A-1745; P-911 to A-1745; F-912 to A-1745; G-913 to A-1745; Y-914 to A-1745; L-915 to A-1745; K-916 to A-1745; I-917 to A-1745; H-918 to A-1745; R-919 to A-1745; L-920 to A-1745; K-921 to A-1745; P-922 to A-1745; S-923 to A-1745; D-924 to A-1745; A-925 to A-1745; G-926 to A-1745; V-927 to A-1745; Y-928 to A-1745; T-929 to A-1745; C-930 to A-1745; S-931 to A-1745; A-932 to A-1745; G-933 to A-1745; P-934 to A-1745; A-935 to A-1745; R-936 to A-1745; E-937 to A-1745; H-938 to A-1745; F-939 to A-1745; V-940 to A-1745; I-941 to A-1745; K-942 to A-1745; L-943 to A-1745; I-944 to A-1745; G-945 to A-1745; G-946 to A-1745; N-947 to A-1745; R-948 to A-1745; K-949 to A-1745; L-950 to A-1745; V-951 to A-1745; A-952 to A-1745; R-953 to A-1745; P-954 to A-1745; L-955 to A-1745; S-956 to A-1745; P-957 to A-1745; R-958 to A-1745; S-959 to A-1745; E-960 to A-1745; E-961 to A-1745; E-962 to A-1745; V-963 to A-1745; L-964 to A-1745; A-965 to A-1745; G-966 to A-1745; R-967 to A-1745; K-968 to A-1745; G-969 to A-1745; G-970 to A-1745; P-971 to A-1745; K-972 to A-1745; E-973 to A-1745; A-974 to A-1745; L-975 to A-1745; Q-976 to A-1745; T-977 to A-1745; H-978 to A-1745; K-979 to A-1745; H-980 to A-1745; Q-981 to A-1745; N-982 to A-1745; G-983 to A-1745; I-984 to A-1745; F-985 to A-1745; S-986 to A-1745; N-987 to A-1745; G-988 to A-1745; S-989 to A-1745; K-990 to A-1745; A-991 to A-1745; E-992 to A-1745; K-993 to A-1745; R-994 to A-1745; G-995 to A-1745; L-996 to A-1745; A-997 to A-1745; A-998 to A-1745; N-999 to A-1745; P-1000 to A-1745; G-1001 to A-1745; S-1002 to A-1745; R-1003 to A-1745; Y-1004 to A-1745; D-1005 to A-1745; D-1006 to A-1745; L-1007 to A-1745; V-1008 to A-1745; S-1009 to A-1745; R-1010 to A-1745; L-1011 to A-1745; L-1012 to A-1745; E-1013 to A-1745; Q-1014 to A-1745; G-1015 to A-1745; G-1016 to A-1745; W-1017 to A-1745; P-1018 to A-1745; G-1019 to A-1745; E-1020 to A-1745; L-1021 to A-1745; L-1022 to A-1745; A-1023 to A-1745; S-1024 to A-1745; W-1025 to A-1745; E-1026 to A-1745; A-1027 to A-1745; Q-1028 to A-1745; D-1029 to A-1745; S-1030 to A-1745; A-1031 to A-1745; E-1032 to A-1745; R-1033 to A-1745; N-1034 to A-1745; T-1035 to A-1745; T-1036 to A-1745; S-1037 to A-1745; E-1038 to A-1745; E-1039 to A-1745; D-1040 to A-1745; P-1041 to A-1745; G-1042 to A-1745; A-1043 to A-1745; E-1044 to A-1745; Q-1045 to A-1745; V-1046 to A-1745; L-1047 to A-1745; L-1048 to A-1745; H-1049 to A-1745; L-1050 to A-1745; P-1051 to A-1745; F-1052 to A-1745; T-1053 to A-1745; M-1054 to A-1745; V-1055 to A-1745; T-1056 to A-1745; E-1057 to A-1745; Q-1058 to A-1745; R-1059 to A-1745; R-1060 to A-1745; L-1061 to A-1745; D-1062 to A-1745; D-1063 to A-1745; I-1064 to A-1745; L-1065 to A-1745; G-1066 to A-1745; N-1067 to A-1745; L-1068 to A-1745; S-1069 to A-1745; Q-1070 to A-1745; Q-1071 to A-1745; P-1072 to A-1745; E-1073 to A-1745; E-1074 to A-1745; L-1075 to A-1745; R-1076 to A-1745; D-1077 to A-1745; L-1078 to A-1745; Y-1079 to A-1745; S-1080 to A-1745; K-1081 to A-1745; H-1082 to A-1745; L-1083 to A-1745; V-1084 to A-1745; A-1085 to A-1745; Q-1086 to A-1745; L-1087 to A-1745; A-1088 to A-1745; Q-1089 to A-1745; E-1090 to A-1745; I-1091 to A-1745; F-1092 to A-1745; R-1093 to A-1745; S-1094 to A-1745; H-1095 to A-1745; L-1096 to A-1745; E-1097 to A-1745; H-1098 to A-1745; Q-1099 to A-1745; D-1100 to A-1745; T-1101 to A-1745; L-1102 to A-1745; L-1103 to A-1745; K-1104 to A-1745; P-1105 to A-1745; S-1106 to A-1745; E-1107 to A-1745; R-1108 to A-1745; R-1109 to A-1745; T-1110 to A-1745; S-1111 to A-1745; P-1112 to A-1745; V-1113 to A-1745; T-1114 to A-1745; L-1115 to A-1745; S-1116 to A-1745; P-1117 to A-1745; H-1118 to A-1745; K-1119 to A-1745; H-1120 to A-1745; V-1121 to A-1745; S-1122 to A-1745; G-1123 to A-1745; F-1124 to A-1745; S-1125 to A-1745; S-1126 to A-1745; S-1127 to A-1745; L-1128 to A-1745; R-1129 to A-1745; T-1130 to A-1745; S-1131 to A-1745; S-1132 to A-1745; T-1133 to A-1745; G-1134 to A-1745; D-1135 to A-1745; A-1136 to A-1745; G-1137 to A-1745; G-1138 to A-1745; G-1139 to A-1745; S-1140 to A-1745; R-1141 to A-1745; R-1142 to A-1745; P-1143 to A-1745; H-1144 to A-1745; R-1145 to A-1745; K-1146 to A-1745; P-1147 to A-1745; T-1148 to A-1745; I-1149 to A-1745; L-1150 to A-1745; R-1151 to A-1745; K-1152 to A-1745; I-1153 to A-1745; S-1154 to A-1745; A-1155 to A-1745; A-1156 to A-1745; Q-1157 to A-1745; Q-1158 to A-1745; L-1159 to A-1745; S-1160 to A-1745; A-1161 to A-1745; S-1162 to A-1745; E-1163 to A-1745; V-1164 to A-1745; V-1165 to A-1745; T-1166 to A-1745; H-1167 to A-1745; L-1168 to A-1745; G-1169 to A-1745; Q-1170 to A-1745; T-1171 to A-1745; V-1172 to A-1745; A-1173 to A-1745; L-1174 to A-1745; A-1175 to A-1745; S-1176 to A-1745; G-1177 to A-1745; T-1178 to A-1745; L-1179 to A-1745; S-1180 to A-1745; V-1181 to A-1745; L-1182 to A-1745; L-1183 to A-1745; H-1184 to A-1745; C-1185 to A-1745; E-1186 to A-1745; A-1187 to A-1745; I-1188 to A-1745; G-1189 to A-1745; H-1190 to A-1745; P-1191 to A-1745; R-1192 to A-1745; P-1193 to A-1745; T-1194 to A-1745; I-1195 to A-1745; S-1196 to A-1745; W-1197 to A-1745; A-1198 to A-1745; R-1199 to A-1745; N-1200 to A-1745; G-1201 to A-1745; E-1202 to A-1745; E-1203 to A-1745; V-1204 to A-1745; Q-1205 to A-1745; F-1206 to A-1745; S-1207 to A-1745; D-1208 to A-1745; R-1209 to A-1745; I-1210 to A-1745; L-1211 to A-1745; L-1212 to A-1745; Q-1213 to A-1745; P-1214 to A-1745; D-1215 to A-1745; D-1216 to A-1745; S-1217 to A-1745; L-1218 to A-1745; Q-1219 to A-1745; I-1220 to A-1745; L-1221 to A-1745; A-1222 to A-1745; P-1223 to A-1745; V-1224 to A-1745; E-1225 to A-1745; A-1226 to A-1745; D-1227 to A-1745; V-1228 to A-1745; G-1229 to A-1745; F-1230 to A-1745; Y-1231 to A-1745; T-1232 to A-1745; C-1233 to A-1745; N-1234 to A-1745; A-1235 to A-1745; T-1236 to A-1745; N-1237 to A-1745; A-1238 to A-1745; L-1239 to A-1745; G-1240 to A-1745; Y-1241 to A-1745; D-1242 to A-1745; S-1243 to A-1745; V-1244 to A-1745; S-1245 to A-1745; I-1246 to A-1745; A-1247 to A-1745; V-1248 to A-1745; T-1249 to A-1745; L-1250 to A-1745; A-1251 to A-1745; G-1252 to A-1745; K-1253 to A-1745; P-1254 to A-1745; L-1255 to A-1745; V-1256 to A-1745; K-1257 to A-1745; T-1258 to A-1745; S-1259 to A-1745; R-1260 to A-1745; M-1261 to A-1745; T-1262 to A-1745; V-1263 to A-1745; I-1264 to A-1745; N-1265 to A-1745; T-1266 to A-1745; E-1267 to A-1745; K-1268 to A-1745; P-1269 to A-1745; A-1270 to A-1745; V-1271 to A-1745; T-1272 to A-1745; V-1273 to A-1745; D-1274 to A-1745; I-1275 to A-1745; G-1276 to A-1745; S-1277 to A-1745; T-1278 to A-1745; I-1279 to A-1745; K-1280 to A-1745; T-1281 to A-1745; V-1282 to A-1745; Q-1283 to A-1745; G-1284 to A-1745; V-1285 to A-1745; N-1286 to A-1745; V-1287 to A-1745; T-1288 to A-1745; I-1289 to A-1745; N-1290 to A-1745; C-1291 to A-1745; Q-1292 to A-1745; V-1293 to A-1745; A-1294 to A-1745; G-1295 to A-1745; V-1296 to A-1745; P-1297 to A-1745; E-1298 to A-1745; A-1299 to A-1745; E-1300 to A-1745; V-1301 to A-1745; T-1302 to A-1745; W-1303 to A-1745; F-1304 to A-1745; R-1305 to A-1745; N-1306 to A-1745; K-1307 to A-1745; S-1308 to A-1745; K-1309 to A-1745; L-1310 to A-1745; G-1311 to A-1745; S-1312 to A-1745; P-1313 to A-1745; H-1314 to A-1745; H-1315 to A-1745; L-1316 to A-1745; H-1317 to A-1745; E-1318 to A-1745; G-1319 to A-1745; S-1320 to A-1745; L-1321 to A-1745; L-1322 to A-1745; L-1323 to A-1745; T-1324 to A-1745; N-1325 to A-1745; V-1326 to A-1745; S-1327 to A-1745; S-1328 to A-1745; S-1329 to A-1745; D-1330 to A-1745; Q-1331 to A-1745; G-1332 to A-1745; L-1333 to A-1745; Y-1334 to A-1745; S-1335 to A-1745; C-1336 to A-1745; R-1337 to A-1745; A-1338 to A-1745; A-1339 to A-1745; N-1340 to A-1745; L-1341 to A-1745; H-1342 to A-1745; G-1343 to A-1745; E-1344 to A-1745; L-1345 to A-1745; T-1346 to A-1745; E-1347 to A-1745; S-1348 to A-1745; T-1349 to A-1745; Q-1350 to A-1745; L-1351 to A-1745; L-1352 to A-1745; I-1353 to A-1745; L-1354 to A-1745; D-1355 to A-1745; P-1356 to A-1745; P-1357 to A-1745; Q-1358 to A-1745; V-1359 to A-1745; P-1360 to A-1745; T-1361 to A-1745; Q-1362 to A-1745; L-1363 to A-1745; E-1364 to A-1745; D-1365 to A-1745; I-1366 to A-1745; R-1367 to A-1745; A-1368 to A-1745; L-1369 to A-1745; L-1370 to A-1745; A-1371 to A-1745; A-1372 to A-1745; T-1373 to A-1745; G-1374 to A-1745; P-1375 to A-1745; N-1376 to A-1745; L-1377 to A-1745; P-1378 to A-1745; S-1379 to A-1745; V-1380 to A-1745; L-1381 to A-1745; T-1382 to A-1745; S-1383 to A-1745; P-1384 to A-1745; L-1385 to A-1745; G-1386 to A-1745; T-1387 to A-1745; Q-1388 to A-1745; L-1389 to A-1745; V-1390 to A-1745; L-1391 to A-1745; D-1392 to A-1745; P-1393 to A-1745; G-1394 to A-1745; N-1395 to A-1745; S-1396 to A-1745; A-1397 to A-1745; L-1398 to A-1745; L-1399 to A-1745; G-1400 to A-1745; C-1401 to A-1745; P-1402 to A-1745; I-1403 to A-1745; K-1404 to A-1745; G-1405 to A-1745; H-1406 to A-1745; P-1407 to A-1745; V-1408 to A-1745; P-1409 to A-1745; N-1410 to A-1745; I-1411 to A-1745; T-1412 to A-1745; W-1413 to A-1745; F-1414 to A-1745; H-1415 to A-1745; G-1416 to A-1745; G-1417 to A-1745; Q-1418 to A-1745; P-1419 to A-1745; I-1420 to A-1745; V-1421 to A-1745; T-1422 to A-1745; A-1423 to A-1745; T-1424 to A-1745; G-1425 to A-1745; L-1426 to A-1745; T-1427 to A-1745; H-1428 to A-1745; H-1429 to A-1745; I-1430 to A-1745; L-1431 to A-1745; A-1432 to A-1745; A-1433 to A-1745; G-1434 to A-1745; Q-1435 to A-1745; I-1436 to A-1745; L-1437 to A-1745; Q-1438 to A-1745; V-1439 to A-1745; A-1440 to A-1745; N-1441 to A-1745; L-1442 to A-1745; S-1443 to A-1745; G-1444 to A-1745; G-1445 to A-1745; S-1446 to A-1745; Q-1447 to A-1745; G-1448 to A-1745; E-1449 to A-1745; F-1450 to A-1745; S-1451 to A-1745; C-1452 to A-1745; L-1453 to A-1745; A-1454 to A-1745; Q-1455 to A-1745; N-1456 to A-1745; E-1457 to A-1745; A-1458 to A-1745; G-1459 to A-1745; V-1460 to A-1745; L-1461 to A-1745; M-1462 to A-1745; Q-1463 to A-1745; K-1464 to A-1745; A-1465 to A-1745; S-1466 to A-1745; L-1467 to A-1745; V-1468 to A-1745; I-1469 to A-1745; Q-1470 to A-1745; D-1471 to A-1745; Y-1472 to A-1745; W-1473 to A-1745; W-1474 to A-1745; S-1475 to A-1745; V-1476 to A-1745; D-1477 to A-1745; R-1478 to A-1745; L-1479 to A-1745; A-1480 to A-1745; T-1481 to A-1745; C-1482 to A-1745; S-1483 to A-1745; A-1484 to A-1745; S-1485 to A-1745; C-1486 to A-1745; G-1487 to A-1745; N-1488 to A-1745; R-1489 to A-1745; G-1490 to A-1745; V-1491 to A-1745; Q-1492 to A-1745; Q-1493 to A-1745; P-1494 to A-1745; R-1495 to A-1745; L-1496 to A-1745; R-1497 to A-1745; C-1498 to A-1745; L-1499 to A-1745; L-1500 to A-1745; N-1501 to A-1745; S-1502 to A-1745; T-1503 to A-1745; E-1504 to A-1745; V-1505 to A-1745; N-1506 to A-1745; P-1507 to A-1745; A-1508 to A-1745; H-1509 to A-1745; C-1510 to A-1745; A-1511 to A-1745; G-1512 to A-1745; K-1513 to A-1745; V-1514 to A-1745; R-1515 to A-1745; P-1516 to A-1745; A-1517 to A-1745; V-1518 to A-1745; Q-1519 to A-1745; P-1520 to A-1745; I-1521 to A-1745; A-1522 to A-1745; C-1523 to A-1745; N-1524 to A-1745; R-1525 to A-1745; R-1526 to A-1745; D-1527 to A-1745; C-1528 to A-1745; P-1529 to A-1745; S-1530 to A-1745; R-1531 to A-1745; W-1532 to A-1745; M-1533 to A-1745; V-1534 to A-1745; T-1535 to A-1745; S-1536 to A-1745; W-1537 to A-1745; S-1538 to A-1745; A-1539 to A-1745; C-1540 to A-1745; T-1541 to A-1745; R-1542 to A-1745; S-1543 to A-1745; C-1544 to A-1745; G-1545 to A-1745; G-1546 to A-1745; G-1547 to A-1745; V-1548 to A-1745; Q-1549 to A-1745; T-1550 to A-1745; R-1551 to A-1745; R-1552 to A-1745; V-1553 to A-1745; T-1554 to A-1745; C-1555 to A-1745; Q-1556 to A-1745; K-1557 to A-1745; L-1558 to A-1745; K-1559 to A-1745; A-1560 to A-1745; S-1536 to A-1745; G-1562 to A-1745; I-1563 to A-1745; S-1564 to A-1745; T-1565 to A-1745; P-1566 to A-1745; V-1567 to A-1745; S-1568 to A-1745; N-1569 to A-1745; D-1570 to A-1745; M-1571 to A-1745; C-1572 to A-1745; T-1573 to A-1745; Q-1574 to A-1745; V-1575 to A-1745; A-1576 to A-1745; K-1577 to A-1745; R-1578 to A-1745; P-15579 to A-1745; V-1580 to A-1745; D-1581 to A-1745; T-1582 to A-1745; Q-1583 to A-1745; A-1584 to A-1745; C-1585 to A-1745; N-1586 to A-1745; Q-1587 to A-1745; Q-1588 to A-1745; L-1589 to A-1745; C-1590 to A-1745; V-1591 to A-1745; E-1592 to A-1745; W-1593 to A-1745; A-1594 to A-1745; F-1595 to A-1745; S-1596 to A-1745; S-1597 to A-1745; W-1598 to A-1745; G-1599 to A-1745; Q-1600 to A-1745; C-1601 to A-1745; N-1602 to A-1745; G-1603 to A-1745; P-1604 to A-1745; C-1605 to A-1745; I-1606 to A-1745; G-1607 to A-1745; P-1608 to A-1745; H-1609 to A-1745; L-1610 to A-1745; A-1611 to A-1745; V-1612 to A-1745; Q-1613 to A-1745; H-1614 to A-1745; R-1615 to A-1745; Q-1616 to A-1745; V-1617 to A-1745; F-1618 to A-1745; C-1619 to A-1745; Q-1620 to A-1745; T-1621 to A-1745; R-1622 to A-1745; D-1623 to A-1745; G-1624 to A-1745; I-1625 to A-1745; T-1626 to A-1745; L-1627 to A-1745; P-1628 to A-1745; S-1629 to A-1745; E-1630 to A-1745; Q-1631 to A-1745; C-1632 to A-1745; S-1633 to A-1745; A-1634 to A-1745; L-1635 to A-1745; P-1636 to A-1745; R-1637 to A-1745; P-1638 to A-1745; V-1639 to A-1745; S-1640 to A-1745; T-1641 to A-1745; Q-1642 to A-1745; N-1643 to A-1745; C-1644 to A-1745; W-1645 to A-1745; S-1646 to A-1745; E-1647 to A-1745; A-1648 to A-1745; C-1649 to A-1745; S-1650 to A-1745; V-1651 to A-1745; H-1652 to A-1745; W-1653 to A-1745; R-1654 to A-1745; V-1655 to A-1745; S-1656 to A-1745; L-1644 to A-1745; W-1658 to A-1745; T-1659 to A-1745; L-1660 to A-1745; C-1661 to A-1745; T-1662 to A-1745; A-1663 to A-1745; T-1664 to A-1745; C-1665 to A-1745; G-1666 to A-1745; N-1667 to A-1745; Y-1668 to A-1745; G-1669 to A-1745; F-1670 to A-1745; Q-1671 to A-1745; S-1672 to A-1745; R-1673 to A-1745; R-1674 to A-1745; V-1675 to A-1745; E-1676 to A-1745; C-1677 to A-1745; V-1678 to A-1745; H-1679 to A-1745; A-1680 to A-1745; R-1681 to A-1745; T-1682 to A-1745; N-1683 to A-1745; K-16684 to A-1745; A-1685 to A-1745; V-1686 to A-1745; P-1687 to A-1745; E-1688 to A-1745; H-1689 to A-1745; L-1690 to A-1745; C-1691 to A-1745; S-1692 to A-1745; W-1693 to A-1745; G-1694 to A-1745; P-1695 to A-1745; R-1696 to A-1745; P-1697 to A-1745; A-1698 to A-1745; N-1699 to A-1745; W-1700 to A-1745; Q-9701 to A-1745; R-1702 to A-1745; C-1703 to A-1745; N-1704 to A-1745; N-1705 to A-1745; T-1706 to A-1745; P-1707 to A-1745; C-1708 to A-1745; E-1709 to A-1745; N-1710 to A-1745; M-1711 to A-1745; E-1712 to A-1745; C-1713 to A-1745; R-1714 to A-1745; D-1715 to A-1745; T-1716 to A-1745; T-1717 to A-1745; R-1718 to A-1745; Y-1719 to A-1745; C-1720 to A-1745; E-1721 to A-1745; K-1722 to A-1745; V-1723 to A-1745; K-1724 to A-1745; Q-1725 to A-1745; L-1726 to A-1745; K-1727 to A-1745; L-1728 to A-1745; C-1729 to A-1745; Q-1730 to A-1745; L-1731 to A-1745; S-1732 to A-1745; Q-1733 to A-1745; F-1734 to A-1745; K-1735 to A-1745; S-1736 to A-1745; R-1737 to A-1745; C-1738 to A-1745; C-1739 to A-1745; and G-1740 to A-1745 of SEQ ID NO: 89. Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
The present invention further provides polypeptides having one or more residues deleted from the carboxy terminus of the amino acid sequence of the THRAP polypeptide shown in FIGS. 4A-4H (SEQ ID NO:89), as described by the general formula 1-n, where n is an integer from 6 to 1745 where n corresponds to the position of amino acid residue identified in SEQ ID NO:89. More in particular, the invention provides polynucleotides encoding polypeptides comprising, or alternatively consisting of, an amino acid sequence selected from the group: E-29 to K-1744; E-29 to G-1743; E-29 to C-1742; E-29 to T-1741; E-29 to G-1740; E-29 to C-1739; E-29 to C-1738; E-29 to R-1737; E-29 to S-1736; E-29 to K-1735; E-29 to F-1734; E-29 to Q-1733; E-29 to S-1732; E-29 to L-1731; E-29 to Q-1730; E-29 to C-1729; E-29 to L-1728; E-29 to K-1727; E-29 to L-1726; E-29 to Q-1725; E-29 to K-1724; E-29 to V-1723; E-29 to K-1722; E-29 to E-1721; E-29 to C-1720; E-29 to Y-1719; E-29 to R-1718; E-29 to T-1717; E-29 to T-1716; E-29 to D-1715; E-29 to R-1714; E-29 to C-1713; E-29 to E-1712; E-29 to E-29711; E-29 to N-1710; E-29 to E-1709; E-29 to C-1708; E-29 to P-1707; E-29 to T-1706; E-29 to I-1705; E-29 to N-1704; E-29 to C-1703; E-29 to R-1702; E-29 to Q-1701; E-29 to W-1700; E-29 to N-1699; E-29 to A-1698; E-29 to P-1697; E-29 to R-1696; E-29 to P-1695; E-29 to G-1694; E-29 to W-1693; E-29 to S-1692; E-29 to C-1691; E-29 to L-1690; E-29 to H-1689; E-29 to E-1688; E-29 to P-1687; E-29 to V-1686; E-29 to A-1685; E-29 to K-1684; E-29 to N-1683; E-29 to T-1682; E-29 to R-1681; E-29 to A-1680; E-29 to H-1679; E-29 to V-1678; E-29 to C-1677; E-29 to E-1676; E-29 to V-1675; E-29 to R-1674; E-29 to R-1673; E-29 to S-1672; E-29 to Q-1671; E-29 to F-1670; E-29 to G-1669; E-29 to Y-1668; E-29 to N-1667; E-29 to G-1666; E-29 to C-1665; E-29 to T-1664; E-29 to A-1663; E-29 to T-1662; E-29 to C-1661; E-29 to L-1660; E-29 to T-1659; E-29 to W-1658; E-29 to L-1657; E-29 to S-1656; E-29 to V-1655; E-29 to R-1654; E-29 to W-1653; E-29 to H-1652; E-29 to V-1651; E-29 to S-1650; E-29 to C-1649; E-29 to A-1648; E-29 to E-1647; E-29 to S-1646; E-29 to W-1645; E-29 to C-1644; E-29 to N-1643; E-29 to Q-1642; E-29 to T-1641; E-29 to S-1640; E-29 to V-1639; E-29 to P-1638; E-29 to R-1637; E-29 to P-1636; E-29 to L-1635; E-29 to A-1634; E-29 to S-1633; E-29 to C-1632; E-29 to Q-1631; E-29 to E-1630; E-29 to S-1629; E-29 to P-1628; E-29 to L-1627; E-29 to T-1626; E-29 to I-1625; E-29 to G-1624; E-29 to D-1623; E-29 to R-1622; E-29 to T-1621; E-29 to Q-1620; E-29 to C-1619; E-29 to F-1618; E-29 to V-1617; E-29 to Q-1616; E-29 to R-1615; E-29 to H-1614; E-29 to Q-1613; E-29 to V-1612; E-29 to A-1611; E-29 to L-1610; E-29 to H-1609; E-29 to P-1608; E-29 to G-1607; E-29 to I-1606; E-29 to C-1605; E-29 to P-1604; E-29 to G-1603; E-29 to N-1602; E-29 to C-1601; E-29 to Q-1600; E-29 to G-1599; E-29 to W-1598; E-29 to S-1597; E-29 to S-1596; E-29 to F-1595; E-29 to A-1594; E-29 to W-1593; E-29 to E-1592; E-29 to V-1591; E-29 to C-1590; E-29 to L-1589; E-29 to Q-1588; E-29 to Q-1587; E-29 to N-1586; E-29 to C-1585; E-29 to A-1584; E-29 to Q-1583; E-29 to T-1582; E-29 to D-1581; E-29 to V-1580; E-29 to P-1579; E-29 to R-1578; E-29 to K-1577; E-29 to A-1576; E-29 to V-1575; E-29 to Q-1574; E-29 to T-1573; E-29 to C-1572; E-29 to E-29571; E-29 to D-1570; E-29 to N-1569; E-29 to S-1568; E-29 to V-1567; E-29 to P-1566; E-29 to T-1565; E-29 to S-1564; E-29 to I-1563; E-29 to G-1562; E-29 to S-2561; E-29 to A-1560; E-29 to K-1559; E-29 to L-1558; E-29 to K-1557; E-29 to Q-1556; E-29 to C-1555; E-29 to T-1554; E-29 to V-1553; E-29 to R-1552; E-29 to R-1551; E-29 to T-1550; E-29 to Q-1549; E-29 to V-1548; E-29 to G-1547; E-29 to G-1546; E-29 to G-1545; E-29 to C-1544; E-29 to S-1543; E-29 to R-1542; E-29 to T-1541; E-29 to C-1540; E-29 to A-1539; E-29 to S-1538; E-29 to W-1537; E-29 to S-1536; E-29 to T-1535; E-29 to V-1534; E-29 to E-29533; E-29 to W-1532; E-29 to R-1531; E-29 to S-1530; E-29 to P-1529; E-29 to C-1528; E-29 to D-1527; E-29 to R-1526; E-29 to R-1525; E-29 to N-1524; E-29 to C-1523; E-29 to A-1522; E-29 to I-1521; E-29 to P-1520; E-29 to Q-1519; E-29 to V-1518; E-29 to A-1517; E-29 to P-1516; E-29 to R-1515; E-29 to V-1514; E-29 to K-1513; E-29 to G-1512; E-29 to A-1511; E-29 to C-1510; E-29 to H-1509; E-29 to A-1508; E-29 to P-1507; E-29 to N-1506; E-29 to V-1505; E-29 to E-1504; E-29 to T-1503; E-29 to S-1502; E-29 to N-1501; E-29 to L-1500; E-29 to L-1499; E-29 to C-1498; E-29 to R-1497; E-29 to L-1496; E-29 to R-1495; E-29 to P-1494; E-29 to Q-1493; E-29 to Q-1492; E-29 to V-1491; E-29 to G-1490; E-29 to R-1489; E-29 to N-1488; E-29 to G-1487; E-29 to C-1486; E-29 to S-1485; E-29 to A-1484; E-29 to S-1483; E-29 to C-1482; E-29 to T-1481; E-29 to A-1480; E-29 to L-1479; E-29 to R-1478; E-29 to D-1477; E-29 to V-1476; E-29 to S-1475; E-29 to W-1474; E-29 to W-1473; E-29 to Y-1472; E-29 to D-1471; E-29 to Q-1470; E-29 to I-1469; E-29 to V-1468; E-29 to L-1467; E-29 to S-1466; E-29 to A-1465; E-29 to K-1464; E-29 to Q-1463; E-29 to E-29462; E-29 to L-1461; E-29 to V-1460; E-29 to G-1459; E-29 to A-1458; E-29 to E-1457; E-29 to N-1456; E-29 to Q-1455; E-29 to A-1454; E-29 to L-1453; E-29 to C-1452; E-29 to S-1451; E-29 to F-1450; E-29 to E-1449; E-29 to G-1448; E-29 to Q-1447; E-29 to S-1446; E-29 to G-1445; E-29 to G-1444; E-29 to S-1443; E-29 to L-1442; E-29 to N-1441; E-29 to A-1440; E-29 to V-1439; E-29 to Q-1438; E-29 to L-1437; E-29 to I-1436; E-29 to Q-1435; E-29 to G-1434; E-29 to A-1433; E-29 to A-1432; E-29 to L-1431; E-29 to I-1430; E-29 to G-1429; E-29 to H-1428; E-29 to T-1427; E-29 to L-1426; E-29 to G-1425; E-29 to T-1424; E-29 to A-1423; E-29 to T-1422; E-29 to V-1421; E-29 to I-1420; E-29 to P-1419; E-29 to Q-1418; E-29 to G-1417; E-29 to G-1416; E-29 to I-1415; E-29 to F-1414; E-29 to W-1413; E-29 to T-1412; E-29 to I-1411; E-29 to N-1410; E-29 to P-1409; E-29 to V-1408; E-29 to P-1407; E-29 to H-1406; E-29 to G-1405; E-29 to K-1404; E-29 to I-1403; E-29 to P-1402; E-29 to C-1401; E-29 to G-1400; E-29 to L-1399; E-29 to L-1398; E-29 to A-1397; E-29 to S-1396; E-29 to N-1395; E-29 to G-1394; E-29 to P-1393; E-29 to D-1392; E-29 to L-1391; E-29 to V-1390; E-29 to L-1389; E-29 to Q-1388; E-29 to T-1387; E-29 to G-1386; E-29 to L-1385; E-29 to P-1384; E-29 to S-1383; E-29 to T-1382; E-29 to L-1381; E-29 to V-1380; E-29 to P-1379; E-29 to P-1378; E-29 to L-1377; E-29 to N-1376; E-29 to P-1375; E-29 to G-1374; E-29 to T-1373; E-29 to A-1372; E-29 to A-1371; E-29 to L-1370; E-29 to L-1369; E-29 to A-1368; E-29 to R-1367; E-29 to I-1366; E-29 to D-1365; E-29 to E-1364; E-29 to L-1363; E-29 to Q-1362; E-29 to T-1361; E-29 to P-1360; E-29 to V-1359; E-29 to Q-1358; E-29 to P-1357; E-29 to P-1356; E-29 to D-1355; E-29 to L-1354; E-29 to I-1353; E-29 to L-1352; E-29 to L-1351; E-29 to Q-1350; E-29 to T-1349; E-29 to S-1348; E-29 to E-1347; E-29 to T-1346; E-29 to L-1345; E-29 to E-1344; E-29 to G-1343; E-29 to H-1342; E-29 to L-1341; E-29 to N-1340; E-29 to A-1339; E-29 to A-1338; E-29 to R-1337; E-29 to C-1336; E-29 to S-1335; E-29 to Y-1334; E-29 to L-1333; E-29 to G-1332; E-29 to Q-1331; E-29 to D-1330; E-29 to S-1329; E-29 to S-1328; E-29 to S-1327; E-29 to V-1326; E-29 to N-1325; E-29 to T-1324; E-29 to L-1323; E-29 to L-1322; E-29 to L-1321; E-29 to S-1320; E-29 to G-1319; E-29 to E-1318; E-29 to H-1317; E-29 to L-1316; E-29 to H-1315; E-29 to H-1314; E-29 to P-1313; E-29 to S-1312; E-29 to G-1311; E-29 to L-1310; E-29 to K-1309; E-29 to S-1308; E-29 to K-1307; E-29 to N-1306; E-29 to R-1305; E-29 to F-1304; E-29 to W-1303; E-29 to T-1302; E-29 to V-1301; E-29 to F-1300; E-29 to A-1299; E-29 to E-1298; E-29 to P-1297; E-29 to V-1296; E-29 to G-1295; E-29 to A-1294; E-29 to V-1293; E-29 to Q-1292; E-29 to C-1291; E-29 to N-1290; E-29 to I-1289; E-29 to T-1288; E-29 to V-1287; E-29 to N-1286; E-29 to V-1285; E-29 to G-1284; E-29 to Q-1283; E-29 to V-1282; E-29 to T-1281; E-29 to K-1280; E-29 to I-1279; E-29 to T-1278; E-29 to S-1277; E-29 to G-1276; E-29 to V-1275; E-29 to D-1274; E-29 to V-1273; E-29 to T-1272; E-29 to V-1271; E-29 to A-1270; E-29 to P-1269; E-29 to K-1268; E-29 to S-1267; E-29 to T-1266; E-29 to N-1265; E-29 to I-1264; E-29 to V-1263; E-29 to T-1262; E-29 to V-29261; E-29 to R-1260; E-29 to S-1259; E-29 to T-1258; E-29 to K-1257; E-29 to V-1256; E-29 to L-1255; E-29 to P-1254; E-29 to K-1253; E-29 to G-1252; E-29 to A-1251; E-29 to L-1250; E-29 to T-1249; E-29 to V-1248; E-29 to A-1247; E-29 to I-1246; E-29 to S-1245; E-29 to V-1244; E-29 to S-1243; E-29 to D-1242; E-29 to Y-1241; E-29 to G-1240; E-29 to L-1239; E-29 to A-1238; E-29 to N-1237; E-29 to T-1236; E-29 to A-1235; E-29 to N-1234; E-29 to C-1233; E-29 to T-1232; E-29 to Y-1231; E-29 to F-1230; E-29 to G-1229; E-29 to V-1228; E-29 to D-1227; E-29 to A-1226; E-29 to F-1225; E-29 to V-1224; E-29 to P-1223; E-29 to A-1222; E-29 to L-1221; E-29 to I-1220; E-29 to Q-1219; E-29 to L-1218; E-29 to S-1217; E-29 to D-1216; E-29 to D-1215; E-29 to P-1214; E-29 to Q-1213; E-29 to L-1212; E-29 to L-1211; E-29 to I-1210; E-29 to R-1209; E-29 to D-1208; E-29 to S-1207; E-29 to F-1206; E-29 to Q-1205; E-29 to V-1204; E-29 to E-1203; E-29 to E-1202; E-29 to G-1201; E-29 to N-1200; E-29 to R-1199; E-29 to A-1198; E-29 to W-1197; E-29 to S-1196; E-29 to I-1195; E-29 to T-1194; E-29 to P-1193; E-29 to R-1192; E-29 to P-1191; E-29 to H-1190; E-29 to G-1189; E-29 to I-1188; E-29 to A-1187; E-29 to E-1186; E-29 to C-1185; E-29 to H-1184; E-29 to L-1183; E-29 to L-1182; E-29 to V-1181; E-29 to S-1180; E-29 to L-1179; E-29 to T-1178; E-29 to G-1177; E-29 to S-1176; E-29 to A-1175; E-29 to L-1174; E-29 to A-1173; E-29 to V-1172; E-29 to T-1171; E-29 to Q-1170; E-29 to G-1169; E-29 to L-1168; E-29 to H-1167; E-29 to T-1166; E-29 to V-1165; E-29 to V-1164; E-29 to E-1163; E-29 to S-1162; E-29 to A-1161; E-29 to S-1160; E-29 to L-1159; E-29 to Q-1158; E-29 to Q-1157; E-29 to A-1156; E-29 to A-1155; E-29 to S-1154; E-29 to I-1153; E-29 to K-1152; E-29 to R-1151; E-29 to L-1150; E-29 to I-1149; E-29 to T-1148; E-29 to P-1147; E-29 to K-1146; E-29 to R-1145; E-29 to H-1144; E-29 to P-1143; E-29 to R-1142; E-29 to R-1141; E-29 to S-1140; E-29 to G-1139; E-29 to G-1138; E-29 to G-1137; E-29 to A-1136; E-29 to D-1135; E-29 to G-1134; E-29 to T-1133; E-29 to S-1132; E-29 to S-1131; E-29 to T-1130; E-29 to R-1129; E-29 to L-1128; E-29 to S-1127; E-29 to S-1126; E-29 to S-1125; E-29 to F-1124; E-29 to G-1123; E-29 to S-1122; E-29 to V-1121; E-29 to H-1120; E-29 to K-1119; E-29 to H-1118; E-29 to P-1117; E-29 to S-1116; E-29 to L-1115; E-29 to T-1114; E-29 to V-1113; E-29 to P-1112; E-29 to S-1111; E-29 to T-1110; E-29 to R-1109; E-29 to R-1108; E-29 to E-1107; E-29 to S-1106; E-29 to P-1105; E-29 to K-1104; E-29 to L-1103; E-29 to L-1102; E-29 to T-1101; E-29 to D-1100; E-29 to Q-1099; E-29 to H-1098; E-29 to E-1097; E-29 to L-1096; E-29 to H-1095; E-29 to S-1094; E-29 to R-1093; E-29 to F-1092; E-29 to I-1091; E-29 to E-1090; E-29 to Q-1089; E-29 to A-1088; E-29 to L-1087; E-29 to Q-1086; E-29 to A-1085; E-29 to V-1084; E-29 to L-1083; E-29 to H-1082; E-29 to K-1081; E-29 to S-1080; E-29 to Y-1079; E-29 to L-1078; E-29 to D-1077; E-29 to R-1076; E-29 to L-1075; E-29 to E-1074; E-29 to E-1073; E-29 to P-1072; E-29 to Q-1071; E-29 to Q-1070; E-29 to S-1069; E-29 to L-1068; E-29 to N-1067; E-29 to G-1066; E-29 to L-1065; E-29 to I-1064; E-29 to D-1063; E-29 to D-1062; E-29 to L-1061; E-29 to R-1060; E-29 to R-1059; E-29 to Q-1058; E-29 to E-1057; E-29 to T-1056; E-29 to V-1055; E-29 to E-29054; E-29 to T-1053; E-29 to F-1052; E-29 to P-1051; E-29 to L-1050; E-29 to H-1049; E-29 to L-1048; E-29 to L-1047; E-29 to V-1046; E-29 to Q-1045; E-29 to E-1044; E-29 to A-1043; E-29 to G-1042; E-29 to P-1041; E-29 to D-1040; E-29 to E-1039; E-29 to E-1038; E-29 to S-1037; E-29 to T-1036; E-29 to T-1035; E-29 to N-1034; E-29 to R-1033; E-29 to E-1032; E-29 to A-1031; E-29 to S-1030; E-29 to D-1029; E-29 to Q-1028; E-29 to A-1027; E-29 to E-1026; E-29 to W-1025; E-29 to S-1024; E-29 to A-1023; E-29 to L-1022; E-29 to L-1021; E-29 to E-1020; E-29 to G-1019; E-29 to P-1018; E-29 to W-1017; E-29 to G-1016; E-29 to G-1015; E-29 to Q-1014; E-29 to E-1013; E-29 to L-1012; E-29 to L-1011; E-29 to R-1010; E-29 to S-1009; E-29 to V-1008; E-29 to L-1007; E-29 to D-1006; E-29 to D-1005; E-29 to Y-1004; E-29 to R-1003; E-29 to S-1002; E-29 to G-1001; E-29 to P-1000; E-29 to N-999; E-29 to A-998; E-29 to A-997; E-29 to L-996; E-29 to G-995; E-29 to R-994; E-29 to K-993; E-29 to E-992; E-29 to A-991; E-29 to K-990; E-29 to S-989; E-29 to G-988; E-29 to N-987; E-29 to S-986; E-29 to F-985; E-29 to I-984; E-29 to G-983; E-29 to N-982; E-29 to Q-981; E-29 to H-980; E-29 to K-979; E-29 to H-978; E-29 to T-977; E-29 to Q-976; E-29 to L-975; E-29 to A-974; E-29 to E-973; E-29 to K-972; E-29 to P-971; E-29 to G-970; E-29 to G-969; E-29 to K-968; E-29 to R-967; E-29 to G-966; E-29 to A-965; E-29 to L-964; E-29 to V-963; E-29 to E-962; E-29 to E-961; E-29 to E-960; E-29 to S-959; E-29 to R-958; E-29 to P-957; E-29 to S-956; E-29 to L-955; E-29 to P-954; E-29 to R-953; E-29 to A-952; E-29 to V-951; E-29 to L-950; E-29 to K-949; E-29 to R-948; E-29 to N-947; E-29 to G-946; E-29 to G-945; E-29 to I-944; E-29 to L-943; E-29 to K-942; E-29 to I-941; E-29 to V-940; E-29 to F-939; E-29 to H-938; E-29 to E-937; E-29 to R-936; E-29 to A-935; E-29 to P-934; E-29 to G-933; E-29 to A-932; E-29 to S-931; E-29 to C-930; E-29 to T-929; E-29 to Y-928; E-29 to V-927; E-29 to G-926; E-29 to A-925; E-29 to D-924; E-29 to S-923; E-29 to P-922; E-29 to K-921; E-29 to L-920; E-29 to R-919; E-29 to H-918; E-29 to I-917; E-29 to K-916; E-29 to L-915; E-29 to Y-914; E-29 to G-913; E-29 to F-912; E-29 to P-911; E-29 to A-910; E-29 to V-909; E-29 to T-908; E-29 to V-907; E-29 to H-906; E-29 to T-905; E-29 to S-904; E-29 to S-903; E-29 to I-902; E-29 to L-901; E-29 to H-900; E-29 to Q-899; E-29 to G-898; E-29 to D-897; E-29 to K-896; E-29 to E-895; E-29 to W-894; E-29 to T-893; E-29 to I-892; E-29 to L-891; E-29 to P-890; E-29 to K-889; E-29 to R-888; E-29 to V-887; E-29 to R-886; E-29 to R-885; E-29 to A-884; E-29 to P-883; E-29 to C-882; E-29 to R-881; E-29 to L-880; E-29 to V-879; E-29 to V-878; E-29 to A-877; E-29 to T-876; E-29 to K-875; E-29 to P-874; E-29 to L-873; E-29 to L-872; E-29 to Y-871; E-29 to A-870; E-29 to F-869; E-29 to G-868; E-29 to G-867; E-29 to V-866; E-29 to V-865; E-29 to F-864; E-29 to H-863; E-29 to L-862; E-29 to K-861; E-29 to R-860; E-29 to Q-859; E-29 to R-858; E-29 to R-857; E-29 to T-856; E-29 to Q-855; E-29 to I-854; E-29 to Y-853; E-29 to V-852; E-29 to K-851; E-29 to R-850; E-29 to A-849; E-29 to A-848; E-29 to A-847; E-29 to I-846; E-29 to H-845; E-29 to P-844; E-29 to S-843; E-29 to H-842; E-29 to K-841; E-29 to T-840; E-29 to S-839; E-29 to P-838; E-29 to R-837; E-29 to G-836; E-29 to P-835; E-29 to R-834; E-29 to A-833; E-29 to C-832; E-29 to T-831; E-29 to A-830; E-29 to L-829; E-29 to M-828; E-29 to C-827; E-29 to P-826; E-29 to R-825; E-29 to I-824; E-29 to S-823; E-29 to S-822; E-29 to S-821; E-29 to F-820; E-29 to P-819; E-29 to L-818; E-29 to P-817; E-29 to P-816; E-29 to C-815; E-29 to L-814; E-29 to T-813; E-29 to S-812; E-29 to N-811; E-29 to V-810; E-29 to V-809; E-29 to T-808; E-29 to S-807; E-29 to L-806; E-29 to G-805; E-29 to T-804; E-29 to K-803; E-29 to L-802; E-29 to M-801; E-29 to K-800; E-29 to R-799; E-29 to C-798; E-29 to I-797; E-29 to A-796; E-29 to S-795; E-29 to R-794; E-29 to T-793; E-29 to Q-792; E-29 to T-791; E-29 to G-790; E-29 to E-789; E-29 to G-788; E-29 to C-787; E-29 to S-786; E-29 to T-785; E-29 to S-784; E-29 to C-783; E-29 to E-782; E-29 to T-781; E-29 to W-780; E-29 to D-779; E-29 to S-778; E-29 to L-777; E-29 to L-776; E-29 to W-775; E-29 to E-774; E-29 to S-773; E-29 to P-772; E-29 to C-771; E-29 to D-770; E-29 to D-769; E-29 to K-768; E-29 to K-767; E-29 to C-766; E-29 to A-765; E-29 to Q-764; E-29 to Q-763; E-29 to C-762; E-29 to A-761; E-29 to P-760; E-29 to K-759; E-29 to S-758; E-29 to A-757; E-29 to S-756; E-29 to C-755; E-29 to F-754; E-29 to T-753; E-29 to E-752; E-29 to P-751; E-29 to L-750; E-29 to E-749; E-29 to L-748; E-29 to F-747; E-29 to S-746; E-29 to G-745; E-29 to D-744; E-29 to A-743; E-29 to M-742; E-29 to R-741; E-29 to Q-740; E-29 to K-739; E-29 to C-738; E-29 to L-737; E-29 to V-736; E-29 to E-735; E-29 to R-734; E-29 to K-733; E-29 to Q-732; E-29 to V-731; E-29 to G-730; E-29 to G-729; E-29 to G-728; E-29 to C-727; E-29 to T-726; E-29 to R-725; E-29 to S-724; E-29 to C-723; E-29 to P-722; E-29 to Q-721; E-29 to W-720; E-29 to Q-719; E-29 to A-718; E-29 to P-717; E-29 to Y-716; E-29 to W-715; E-29 to A-714; E-29 to P-713; E-29 to P-712; E-29 to C-711; E-29 to N-710; E-29 to F-709; E-29 to R-708; E-29 to N-707; E-29 to C-706; E-29 to A-705; E-29 to Q-704; E-29 to V-703; E-29 to T-702; E-29 to S-701; E-29 to P-700; E-29 to K-699; E-29 to P-698; E-29 to Q-697; E-29 to R-696; E-29 to C-695; E-29 to L-694; E-29 to E-693; E-29 to D-692; E-29 to A-691; E-29 to L-690; E-29 to I-689; E-29 to V-688; E-29 to T-687; E-29 to E-686; E-29 to N-685; E-29 to M-684; E-29 to E-683; E-29 to R-682; E-29 to S-681; E-29 to L-680; E-29 to L-679; E-29 to H-678; E-29 to S-677; E-29 to C-676; E-29 to F-675; E-29 to V-674; E-29 to D-673; E-29 to R-672; E-29 to T-671; E-29 to Q-670; E-29 to L-669; E-29 to G-668; E-29 to V-667; E-29 to G-666; E-29 to C-665; E-29 to T-664; E-29 to L-663; E-29 to S-662; E-29 to C-661; E-29 to P-660; E-29 to S-659; E-29 to W-658; E-29 to K-657; E-29 to G-656; E-29 to I-655; E-29 to E-654; E-29 to W-653; E-29 to R-652; E-29 to A-651; E-29 to P-650; E-29 to C-649; E-29 to P-648; E-29 to D-647; E-29 to L-646; E-29 to N-645; E-29 to C-644; E-29 to S-643; E-29 to K-642; E-29 to L-641; E-29 to L-640; E-29 to Q-639; E-29 to P-638; E-29 to P-637; E-29 to R-636; E-29 to R-635; E-29 to S-634; E-29 to T-633; E-29 to V-632; E-29 to C-631; E-29 to L-630; E-29 to N-629; E-29 to E-628; E-29 to E-627; E-29 to A-626; E-29 to P-625; E-29 to E-624; E-29 to R-623; E-29 to T-622; E-29 to Q-621; E-29 to K-620; E-29 to N-619; E-29 to L-618; E-29 to C-617; E-29 to S-616; E-29 to V-615; E-29 to V-614; E-29 to A-613; E-29 to E-612; E-29 to Q-611; E-29 to V-610; E-29 to G-609; E-29 to G-608; E-29 to G-607; E-29 to C-606; E-29 to S-605; E-29 to E-604; E-29 to S-603; E-29 to C-602; E-29 to K-601; E-29 to T-600; E-29 to F-599; E-29 to G-598; E-29 to E-597; E-29 to Y-596; E-29 to E-595; E-29 to W-594; E-29 to D-593; E-29 to Y-592; E-29 to L-591; E-29 to E-590; E-29 to D-589; E-29 to F-588; E-29 to D-587; E-29 to Q-586; E-29 to L-585; E-29 to G-584; E-29 to G-583; E-29 to F-582; E-29 to L-581; E-29 to G-580; E-29 to D-579; E-29 to T-578; E-29 to E-577; E-29 to D-576; E-29 to P-575; E-29 to N-574; E-29 to F-573; E-29 to E-572; E-29 to P-571; E-29 to I-570; E-29 to E-569; E-29 to G-568; E-29 to S-567; E-29 to C-566; E-29 to P-565; E-29 to G-564; E-29 to A-563; E-29 to Y-562; E-29 to C-561; E-29 to A-560; E-29 to R-559; E-29 to Q-558; E-29 to S-557; E-29 to A-556; E-29 to P-555; E-29 to K-554; E-29 to P-553; E-29 to G-552; E-29 to E-551; E-29 to C-550; E-29 to E-549; E-29 to D-548; E-29 to I-547; E-29 to P-546; E-29 to L-545; E-29 to D-544; E-29 to A-543; E-29 to V-542; E-29 to S-541; E-29 to Q-540; E-29 to S-539; E-29 to F-538; E-29 to S-537; E-29 to L-536; E-29 to L-535; E-29 to V-534; E-29 to Q-533; E-29 to C-532; E-29 to R-531; E-29 to V-530; E-29 to I-529; E-29 to R-528; E-29 to V-527; E-29 to Q-526; E-29 to T-525; E-29 to G-524; E-29 to V-523; E-29 to G-522; E-29 to C-521; E-29 to T-520; E-29 to V-519; E-29 to T-518; E-29 to C-517; E-29 to A-516; E-29 to S-515; E-29 to W-514; E-29 to A-513; E-29 to K-512; E-29 to P-511; E-29 to I-510; E-29 to F-509; E-29 to S-508; E-29 to P-507; E-29 to E-506; E-29 to E-505; E-29 to S-504; E-29 to V-503 E-29 to A-502; E-29 to A-501; E-29 to G-500; E-29 to E-499; E-29 to E-498; E-29 to L-497; E-29 to E-496; E-29 to Q-495; E-29 to A-494; E-29 to Q-493; E-29 to K-492; E-29 to F-491; E-29 to W-490; E-29 to P-489; E-29 to L-488; E-29 to K-487; E-29 to A-486; E-29 to E-485; E-29 to V-484; E-29 to P-483; E-29 to L-482; E-29 to K-481; E-29 to E-480; E-29 to K-479; E-29 to P-478; E-29 to K-477; E-29 to Y-476; E-29 to C-475; E-29 to P-474; E-29 to T-473; E-29 to P-472; E-29 to V-471; E-29 to I-470; E-29 to C-469; E-29 to E-468; E-29 to E-467; E-29 to K-466; E-29 to I-465; E-29 to H-464; E-29 to P-463; E-29 to K-462; E-29 to T-461; E-29 to K-460; E-29 to P-459; E-29 to S-458; E-29 to C-457; E-29 to G-456; E-29 to G-455; E-29 to T-454; E-29 to H-453; E-29 to M-452; E-29 to G-451; E-29 to R-450; E-29 to H-449; E-29 to D-448; E-29 to I-447; E-29 to C-446; E-29 to L-445; E-29 to V-444; E-29 to V-443; E-29 to R-442; E-29 to Y-441; E-29 to R-440; E-29 to L-439; E-29 to G-438; E-29 to Q-437; E-29 to G-436; E-29 to C-435; E-29 to T-434; E-29 to V-433; E-29 to T-432; E-29 to C-431; E-29 to P-430; E-29 to S-429; E-29 to W-428; E-29 to G-427; E-29 to Q-426; E-29 to A-425; E-29 to L-424; E-29 to W-423; E-29 to K-422; E-29 to P-421; E-29 to C-420; E-29 to D-419; E-29 to F-418; E-29 to I-417; E-29 to N-416; E-29 to C-415; E-29 to P-414; E-29 to Q-413; E-29 to A-412; E-29 to I-411; E-29 to P-410; E-29 to M-409; E-29 to K-408; E-29 to P-407; E-29 to I-406; E-29 to Y-405; E-29 to M-404; E-29 to C-403; E-29 to K-402; E-29 to W-401; E-29 to E-400; E-29 to P-399; E-29 to V-398; E-29 to S-397; E-29 to T-396; E-29 to V-395; E-29 to H-394; E-29 to G-393; E-29 to Q-392; E-29 to I-391; E-29 to D-390; E-29 to E-389; E-29 to E-388; E-29 to V-387; E-29 to C-386; E-29 to S-385; E-29 to V-384; E-29 to A-383; E-29 to R-382; E-29 to S-381; E-29 to Q-380; E-29 to I-379; E-29 to G-378; E-29 to G-377; E-29 to G-376; E-29 to C-375; E-29 to S-374; E-29 to S-373; E-29 to S-372; E-29 to C-371; E-29 to A-370; E-29 to T-369; E-29 to W-368; E-29 to P-367; E-29 to T-366; E-29 to A-365; E-29 to E-364; E-29 to W-363; E-29 to R-362; E-29 to A-361; E-29 to P-360; E-29 to C-359; E-29 to P-358; E-29 to D-357; E-29 to L-356; E-29 to N-355; E-29 to C-354; E-29 to E-353; E-29 to Q-352; E-29 to L-351; E-29 to K-350; E-29 to P-349; E-29 to K-348; E-29 to P-347; E-29 to K-346; E-29 to I-345; E-29 to N-344; E-29 to E-343; E-29 to P-342; E-29 to Y-341; E-29 to Y-340; E-29 to H-339; E-29 to C-338; E-29 to Y-337; E-29 to Q-336; E-29 to D-335; E-29 to A-334; E-29 to V-333; E-29 to V-332; E-29 to R-331; E-29 to N-330; E-29 to S-329; E-29 to R-328; E-29 to L-327; E-29 to D-326; E-29 to Y-325; E-29 to C-324; E-29 to E-323; E-29 to A-322; E-29 to S-321; E-29 to T-320; E-29 to L-319; E-29 to Q-318; E-29 to Y-317; E-29 to G-316; E-29 to G-315; E-29 to G-314; E-29 to C-313; E-29 to T-312; E-29 to A-311; E-29 to S-310; E-29 to C-309; E-29 to P-308; E-29 to F-307; E-29 to F-306; E-29 to D-305; E-29 to T-304; E-29 to E-303; E-29 to R-302; E-29 to W-301; E-29 to R-300; E-29 to H-299; E-29 to I-298; E-29 to I-297; E-29 to P-296; E-29 to Q-295; E-29 to Y-294; E-29 to F-293; E-29 to I-292; E-29 to F-291; E-29 to Q-290; E-29 to V-289; E-29 to T-288; E-29 to S-287; E-29 to D-286; E-29 to A-285; E-29 to S-284; E-29 to G-283; E-29 to S-282; E-29 to N-281; E-29 to R-280; E-29 to I-279; E-29 to K-278; E-29 to V-277; E-29 to I-276; E-29 to F-275; E-29 to D-274; E-29 to A-273; E-29 to T-272; E-29 to L-271; E-29 to P-270; E-29 to G-269; E-29 to A-268; E-29 to M-267; E-29 to R-266; E-29 to L-265; E-29 to I-264; E-29 to E-263; E-29 to K-262; E-29 to D-261; E-29 to P-260; E-29 to F-259; E-29 to K-258; E-29 to Q-257; E-29 to F-256; E-29 to D-255; E-29 to V-254; E-29 to S-253; E-29 to S-252; E-29 to N-251; E-29 to D-250; E-29 to V-249; E-29 to L-248; E-29 to F-247; E-29 to T-246; E-29 to G-245; E-29 to T-244; E-29 to S-243; E-29 to S-242; E-29 to L-241; E-29 to S-240; E-29 to N-239; E-29 to E-238; E-29 to G-237; E-29 to K-236; E-29 to T-235; E-29 to G-234; E-29 to Q-233; E-29 to L-232; E-29 to T-231; E-29 to K-230; E-29 to T-229; E-29 to E-228; E-29 to L-227; E-29 to Y-226; E-29 to L-225; E-29 to H-224; E-29 to D-223; E-29 to P-222; E-29 to G-221; E-29 to K-220; E-29 to L-219; E-29 to V-218; E-29 to L-217; E-29 to R-216; E-29 to I-215; E-29 to H-214; E-29 to R-213; E-29 to S-212; E-29 to G-211; E-29 to Y-210; E-29 to P-209; E-29 to I-208; E-29 to A-207; E-29 to V-206; E-29 to V-205; E-29 to T-204; E-29 to D-203; E-29 to D-202; E-29 to S-201; E-29 to K-200; E-29 to T-199; E-29 to A-198; E-29 to S-197; E-29 to L-196; E-29 to Q-195; E-29 to S-194; E-29 to K-193; E-29 to Y-192; E-29 to Q-191; E-29 to G-190; E-29 to R-189; E-29 to V-188; E-29 to L-187; E-29 to R-186; E-29 to C-185; E-29 to T-184; E-29 to S-183; E-29 to G-182; E-29 to D-181; E-29 to G-180; E-29 to N-179; E-29 to C-178; E-29 to V-177; E-29 to G-176; E-29 to C-175; E-29 to N-174; E-29 to D-173; E-29 to E-172; E-29 to K-171; E-29 to V-170; E-29 to T-169; E-29 to S-168; E-29 to G-167; E-29 to L-166; E-29 to Q-165; E-29 to H-164; E-29 to D-163; E-29 to C-162; E-29 to G-161; E-29 to V-160; E-29 to I-159; E-29 to Q-158; E-29 to C-157; E-29 to L-156; E-29 to G-155; E-29 to S-154; E-29 to I-153; E-29 to C-152; E-29 to E-2951 E-29 to D-150; E-29 to L-149; E-29 to S-148; E-29 to E-147; E-29 to T-146; E-29 to Y-145; E-29 to C-144; E-29 to R-143; E-29 to T-142; E-29 to G-141; E-29 to D-140; E-29 to L-139; E-29 to V-138; E-29 to K-137; E-29 to P-136; E-29 to A-135; E-29 to L-134; E-29 to E-133; E-29 to V-132; E-29 to V-131; E-29 to L-130; E-29 to T-129; E-29 to T-128; E-29 to G-127; E-29 to K-126; E-29 to A-125; E-29 to Q-124; E-29 to C-123; E-29 to K-122; E-29 to L-121; E-29 to S-120; E-29 to C-119; E-29 to P-118; E-29 to N-117; E-29 to D-116; E-29 to P-115; E-29 to D-114; E-29 to N-113; E-20 to S-112; E-29 to V-111; E-29 to P-110; E-29 to L-109; E-29 to W-108; E-29 to E-107; E-29 to Y-106; E-29 to F-105; E-29 to Q-104; E-29 to G-103; E-29 to H-102; E-29 to H-101; E-29 to K-100; E-29 to V-99; E-29 to D-98; E-29 to N-97; E-29 to H-96; E-29 to A-95; E-29 to S-94; E-29 to C-93; E-29 to Q-92; E-29 to Q-91; E-29 to A-90; E-29 to R-89; E-29 to F-88; E-29 to D-87; E-29 to G-86; E-29 to A-85; E-29 to E-84; E-29 to P-83; E-29 to P-82; E-29 to C-81; E-29 to D-80; E-29 to V-79; E-29 to N-78; E-29 to S-77; E-29 to C-76; E-29 to T-75; E-29 to R-74; E-29 to Y-73; E-29 to R-72; E-29 to I-71; E-29 to N-70; E-29 to R-69; E-29 to G-68; E-29 to E-67; E-29 to C-66; E-29 to S-65; E-29 to K-64; E-29 to S-63; E-29 to S-62; E-29 to L-61; E-29 to C-60; E-29 to R-59; E-29 to R-58; E-29 to L-57; E-29 to S-56; E-29 to Y-55; E-29 to S-54; E-29 to A-53; E-29 to G-52; E-29 to G-51; E-29 to G-50; E-29 to C-49; E-29 to T-48; E-29 to R-47; E-29 to S-46; E-29 to C-45; E-29 to E-44; E-29 to S-43; E-29 to W-42; E-29 to P-41; E-29 to G-40; E-29 to W-39; E-29 to A-38; E-29 to D-37; E-29 to W-36; E-29 to L-35; E-29 to G-34; E-29 to D-33; E-29 to R-32; E-29 to D-31; or E-29 to E-30 of SEQ ID NO:89. Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Moreover, a signal sequence may be added to these C-terminal constructs. For example, amino acids 1-28 of SEQ ID NO:89, amino acids 2-28 of SEQ ID NO:89, amino acids 3-28 of SEQ ID NO:89, amino acids 4-28 of SEQ ID NO:89, amino acids 5-28 of SEQ ID NO:89, amino acids 6-28 of SEQ ID NO:89, amino acids 7-28 of SEQ ID NO:89, amino acids 8-28 of SEQ ID NO:89, amino acids 9-28 of SEQ ID NO:89, amino acids 10-28 of SEQ ID NO:89, amino acids 11-28 of SEQ ID NO:89, amino acids 12-28 of SEQ ID NO:89, amino acids 13-28 of SEQ ID NO:89, amino acids 14-28 of SEQ ID NO:89, amino acids 15-28 of SEQ ID NO:89, amino acids 16-28 of SEQ ID NO:89, amino acids 17-28 of SEQ ID NO:89, amino acids 18-28 of SEQ ID NO:89, amino acids 19-28 of SEQ ID NO:89, amino acids 20-28 of SEQ ID NO:89, amino acids 21-28 of SEQ ID NO:89, amino acids 22-28 of SEQ ID NO:89, amino acids 23-28 of SEQ ID NO:89, amino acids 24-28 of SEQ ID NO:89, amino acids 25-28 of SEQ ID NO:89, amino acids 26-28 of SEQ ID NO:89, or amino acids 27-28 of SEQ ID NO:89 can be added to the N-terminus of each C-terminal constructs listed above.
In addition, any of the above listed N- or C-terminal deletions can be combined to produce a N- and C-terminal deleted THRAP polypeptide. The invention also provides polypeptides having one or more amino acids deleted from both the amino and the carboxyl termini, which may be described generally as having residues m-n of SEQ ID NO:89, where n and m are integers as described above. It is understood, however, that any N- and C-terminal deletion mutant is at least, preferably, 6 amino acids, 10 amino acids, 20 amino acids, or 50 amino acids in length. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Moreover, the invention provides nucleic acid molecules having nucleotide sequences related to extensive portions of SEQ ID NO:18 which have been determined from the following related cDNA clones: HBINE55R (SEQ ID NO:156), HOEEW19R (SEQ ID NO:157), HSLAS01R (SEQ ID NO:158), HORBP08R (SEQ ID NO:159)and HAJBI67R (SEQ ID NO:160).
Also preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: TSP-1-like domain1; TSP-1-like domain1 and the proteinase domain; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain3; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain4; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain5; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain6; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain7; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain8; TSP-1-like domain1, the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain9; TSP-1-like domain1, the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, and the IgG-like domain; TSP-1-like domain1, the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the TgG-like domain and the TSP-1-like domain10; TSP-1-like domain1, the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10, and the TSP-1-like domain 11; TSP-1-like domain1, the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or TSP-1-like domain1, the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the proteinase domain; the proteinase domain, and the TSP-1-like domain2; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain3; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain4; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain5; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain6; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain7; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain8; the proteinase domain, and the TSP-1-like domain2 to TSP-1-like domain9; the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, and the IgG-like domain; the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the proteinase domain, the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: TSP-1-like domain2; the TSP-1-like domain2 to TSP-1-like domain3; the TSP-1-like domain2 to TSP-1-like domain4; the TSP-1-like domain2 to TSP-1-like domain5; the TSP-1-like domain2 to TSP-1-like domain6; the TSP-1-like domain2 to TSP-1-like domain7; the TSP-1-like domain2 to TSP-1-like domain8; the TSP-1-like domain2 to TSP-1-like domain9; the TSP-1-like domain2 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain2 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain3; the TSP-1-like domain3 to TSP-1-like domain4; the TSP-1-like domain3 to TSP-1-like domain5; the TSP-1-like domain3 to TSP-1-like domain6; the TSP-1-like domain3 to TSP-1-like domain7; the TSP-1-like domain3 to TSP-1-like domain8; the TSP-1-like domain3 to TSP-1-like domain9; the TSP-1-like domain3 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain3 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain3 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain3 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain3 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain4; the TSP-1-like domain4 to TSP-1-like domain5; the TSP-1-like domain4 to TSP-1-like domain6; the TSP-1-like domain4 to TSP-1-like domain7; the TSP-1-like domain4 to TSP-1-like domain8; the TSP-1-like domain4 to TSP-1-like domain9; the TSP-1-like domain4 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain4 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain4 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain4 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain4 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain5; the TSP-1-like domain5 to TSP-1-like domain6; the TSP-1-like domain5 to TSP-1-like domain7; the TSP-1-like domain5 to TSP-1-like domain8; the TSP-1-like domain5 to TSP-1-like domain9; the TSP-1-like domain5 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain5 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain5 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain5 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain5 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain6; the TSP-1-like domain6 to TSP-1-like domain7; the TSP-1-like domain6 to TSP-1-like domain8; the TSP-1-like domain6 to TSP-1-like domain9; the TSP-1-like domain6 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain6 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain6 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain6 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain6 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain7; the TSP-1-like domain7 to TSP-1-like domain8; the TSP-1-like domain7 to TSP-1-like domain9; the TSP-1-like domain7 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain7 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain7 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain7 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain7 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain8; the TSP-1-like domain8 to TSP-1-like domain9; the TSP-1-like domain8 to TSP-1-like domain9, and the IgG-like domain; the TSP-1-like domain8 to TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain8 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain8 to TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain8 to TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain9; TSP-1-like domain9 and the IgG-like domain; the TSP-1-like domain9, the IgG-like domain and the TSP-1-like domain10; the TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain9, the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the TSP-1-like domain9, the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the IgG-like domain; the IgG-like domain and the TSP-1-like domain10; the IgG-like domain, the TSP-1-like domain10 and the TSP-1-like domain11; the IgG-like domain, the TSP-1-like domain10 to the TSP-1-like domain12; or the IgG-like domain, and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain10; the TSP-1-like domain10 and the TSP-1-like domain11; the TSP-1-like domain10 to the TSP-1-like domain12; and the TSP-1-like domain10 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain11; the TSP-1-like domain11 to the TSP-1-like domain12; and the TSP-1-like domain11 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragment: the TSP-1-like domain12; or the TSP-1-like domain12 to the TSP-1-like domain13.
Additionally, preferred polypeptide fragments of the invention comprise, or consist of, the following fragments: the TSP-1-like domain13.
Also included are a nucleotide sequence encoding a polypeptide consisting of a portion of the complete THRAP amino acid sequence encoded by the cDNA clone (HOHCA60) contained in ATCC(copyright) Deposit No. PTA-627, where this portion excludes any integer of amino acid residues from 1 to about 1735 amino acids from the amino terminus of the complete amino acid sequence encoded by the cDNA clone contained in ATCC(copyright) Deposit No. PTA-627, or any integer of amino acid residues from 1 to about 1735 amino acids from the carboxy terminus, or any combination of the above amino terminal and carboxy terminal deletions, of the complete amino acid sequence encoded by the cDNA clone contained in ATCC(copyright) Deposit No. PTA-627. Polynucleotides encoding all of the above deletion mutant polypeptide forms are also encompassed by the invention.
In additional embodiments, the polynucleotides of the invention encode functional attributes of THRAP. Preferred embodiments of the invention in this regard include fragments that comprise alpha-helix and alpha-helix forming regions (xe2x80x9calpha-regionsxe2x80x9d), beta-sheet and beta-sheet forming regions (xe2x80x9cbeta-regionsxe2x80x9d), turn and turn-forming regions (xe2x80x9cturn-regionsxe2x80x9d), coil and coil-forming regions (xe2x80x9ccoil-regionsxe2x80x9d), hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions and high antigenic index regions of THRAP.
The data representing the structural or functional attributes of THRAP set forth in FIGS. 4A-4H and/or Table 7, as described above, was generated using the various modules and algorithms of the DNA*STAR set on default parameters. In a preferred embodiment, the data presented in columns VIII, IX, XIII, and XIV of Table 7 can be used to determine regions of THRAP which exhibit a high degree of potential for antigenicity. Regions of high antigenicity are determined from the data presented in columns VIII, IX, XIII, and/or IV by choosing values which represent regions of the polypeptide which are likely to be exposed on the surface of the polypeptide in an environment in which antigen recognition may occur in the process of initiation of an immune response. The columns are labeled with the headings xe2x80x9cResxe2x80x9d, xe2x80x9cPositionxe2x80x9d, and Roman Numerals I-XIV. The column headings refer to the following features of the amino acid sequence presented in FIGS. 4A-H, and Table 7: xe2x80x9cResxe2x80x9d: amino acid residue of SEQ ID NO: 89 and FIGS. 4A-4H; xe2x80x9cPositionxe2x80x9d: position of the corresponding residue within SEQ ID NO: 89 and FIGS. 4A-4H; I: Alpha, Regionsxe2x80x94Garnier-Robson; II: Alpha, Regionsxe2x80x94Chou-Fasman; III: Beta, Regionsxe2x80x94Garnier-Robson; IV: Beta, Regionsxe2x80x94Chou-Fasman; V: Turn, Regionsxe2x80x94Garnier-Robson; VI: Turn, Regionsxe2x80x94Chou-Fasman; VII: Coil, Regionsxe2x80x94Garnier-Robson; VIII: Hydrophilicity Plotxe2x80x94Kyte-Doolittle; IX: Hydrophobicity Plotxe2x80x94Hopp-Woods; X: Alpha, Amphipathic Regionsxe2x80x94Eisenberg; XI: Beta, Amphipathic Regionsxe2x80x94Eisenberg; XII: Flexible Regionsxe2x80x94Karplus-Schulz; XIII: Antigenic Indexxe2x80x94Jameson-Wolf; and XIV: Surface Probability Plotxe2x80x94Emini.
Certain preferred regions in these regards are set out in FIG. 6, but may, as shown in Table 7, be represented or identified by using tabular representations of the data presented in FIG. 6. The DNA*STAR computer algorithm used to generate FIG. 6 (set on the original default parameters) was used to present the data in FIG. 6 in a tabular format (See Table 7). The tabular format of the data in FIG. 6 may be used to easily determine specific boundaries of a preferred region.
The above-mentioned preferred regions set out in FIG. 6 and in Table 7 include, but are not limited to, regions of the aforementioned types identified by analysis of the amino acid sequence set out in FIGS. 4A-4H. As set out in FIG. 6 and in Table 7, such preferred regions include Garnier-Robson alpha-regions, beta-regions, turn-regions, and coil-regions, Chou-Fasman alpha-regions, beta-regions, and coil-regions, Kyte-Doolittle hydrophilic regions and hydrophobic regions, Eisenberg alpha- and beta-amphipathic regions, Karplus-Schulz flexible regions, Emini surface-forming regions and Jameson-Wolf regions of high antigenic index.
Also preferred are THRAP polypeptide variants. For example, site directed changes at the amino acid level of THRAP (SEQ ID NO:89) can be made by replacing a particular amino acid with a conservative amino acid. Preferred conservative substitutions include: MI replaced with A, G, I, L, S, T, or V; E2 replaced with D; R5 replaced with H, or K; R6 replaced with H, or K; A7 replaced with G, I, L, S, T, M, or V; T8 replaced with A, G, I, L, S, M, or V; G10 replaced with A, I, L, S, T, M, or V; T11 replaced with A, G, I, L, S, M, or V; L12 replaced with A, G, I, S, T, M, or V; L13 replaced with A, G, I, S, T, M, or V; L14 replaced with A, G, I, S, T, M, or V; F15 replaced with W, or Y; L16 replaced with A, G, I, S, T, M, or V; A17 replaced with G, I, L, S, T, M, or V; F18 replaced with W, or Y; L19 replaced with A, G, I, S, T, M, or V; L20 replaced with A, G, I, S, T, M, or V; L21 replaced with A, G, I, S, T, M, or V; S22 replaced with A, G, I, L, T, M, or V; S23 replaced with A, G, I, L, T, M, or V; R24 replaced with H, or K; T25 replaced with A, G, I, L, S, M, or V; A26 replaced with G, I, L, S, T, M, or V; R27 replaced with H, or K; S28 replaced with A, G, I, L, T, M, or V; E29 replaced with D; E30 replaced with D; D31 replaced with E; R32 replaced with H, or K; D33 replaced with E; G34 replaced with A, I, L, S, T, M, or V; L35 replaced with A, G, I, S, T, M, or V; W36 replaced with F, or Y; D37 replaced with E; A38 replaced with G, I, L, S, T, M, or V; W39 replaced with F, or Y; G40 replaced with A, I, L, S, T, M, or V; W42 replaced with F, or Y; S43 replaced with A, G, I, L, T, M, or V; E44 replaced with D; S46 replaced with A, G, I, L, T, M, or V; R47 replaced with H, or K; T48 replaced with A, G, I, L, S, M, or V; G50 replaced with A, I, L, S, T, M, or V; G51 replaced with A, I, L, S, T, M, or V; G52 replaced with A, I, L, S, T, M, or V; A53 replaced with G, I, L, S, T, M, or V; S54 replaced with A, G, I, L, T, M, or V; Y55 replaced with F, or W; S56 replaced with A, G, I, L, T, M, or V; L57 replaced with A, G, I, S, T, M, or V; R58 replaced with H, or K; R59 replaced with H, or K; L61 replaced with A, G, I, S, T, M, or V; S62 replaced with A, G, I, L, T, M, or V; S63 replaced with A, G, I, L, T, M, or V; K64 replaced with H, or R; S65 replaced with A, G, I, L, T, M, or V; E67 replaced with D; G68 replaced with A, I, L, S, T, M, or V; R69 replaced with H, or K; N70 replaced with Q; I71 replaced with A, G, L, S, T, M, or V; R72 replaced with H, or K; Y73 replaced with F, or W; R74 replaced with H, or K; T75 replaced with A, G, I, L, S, M, or V; S77 replaced with A, G, I, L, T, M, or V; N78 replaced with Q; V79 replaced with A, G, I, L, S, T, or M; D80 replaced with E; E84 replaced with D; A85 replaced with G, I, L, S, T, M, or V; G86 replaced with A, I, L, S, T, M, or V; D87 replaced with E; F88 replaced with W, or Y; R89 replaced with H, or K; A90 replaced with G, I, L, S, T, M, or V; Q91 replaced with N; Q92 replaced with N; S94 replaced with A, G, I, L, T, M, or V; A95 replaced with G, I, L, S, T, M, or V; H96 replaced with K, or R; N97 replaced with Q; D98 replaced with E; V99 replaced with A, G, I, L, S, T, or M; K100 replaced with H, or R; H101 replaced with K, or R; H102 replaced with K, or R; G103 replaced with A, I, L, S, T, M, or V; Q104 replaced with N; F105 replaced with W, or Y; Y106 replaced with F, or W; E107 replaced with D; W108 replaced with F, or Y; L109 replaced with A, G, I, S, T, M, or V; V111 replaced with A, G, I, L, S, T, or M; S112 replaced with A, G, I, L, T, M, or V; N113 replaced with Q; D114 replaced with E; D116 replaced with E; N117 replaced with Q; S120 replaced with A, G, I, L, T, M, or V; L121 replaced with A, G, I, S, T, M, or V; K122 replaced with H, or R; Q124 replaced with N; A125 replaced with G, I, L, S, T, M, or V; K126 replaced with H, or R; G127 replaced with A, I, L, S, T, M, or V; T128 replaced with A, G, I, L, S, M, or V; T129 replaced with A, G, I, L, S, M, or V; L130 replaced with A, G, I, S, T, M, or V; V131 replaced with A, G, I, L, S, T, or M; V132 replaced with A, G, I, L, S, T, or M; E133 replaced with D; L134 replaced with A, G, I, S, T, M, or V; A135 replaced with G, I, L, S, T, M, or V; K137 replaced with H, or R; V138 replaced with A, G, I, L, S, T, or M; L139 replaced with A, G, I, S, T, M, or V; D140 replaced with E; G141 replaced with A, I, L, S, T, M, or V; T142 replaced with A, G, I, L, S, M, or V; R143 replaced with H, or K; Y145 replaced with F, or W; T146 replaced with A, G, I, L, S, M, or V; E147 replaced with D; S148 replaced with A, G, I, L, T, M, or V; L149 replaced with A, G, I, S, T, M, or V; D150 replaced with E; M151 replaced with A, G, I, L, S, T, or V; I153 replaced with A, G, L, S, T, M, or V; S154 replaced with A, G, I, L, T, M, or V; G155 replaced with A, I, L, S, T, M, or V; L156 replaced with A, G, I, S, T, M, or V; Q158 replaced with N; I159 replaced with A, G, L, S, T, M, or V; V160 replaced with A, G, I, L, S, T, or M; G161 replaced with A, I, L, S, T, M, or V; D 163 replaced with E; H 164 replaced with K, or R; Q165 replaced with N; L166 replaced with A, G, I, S, T, M, or V; G167 replaced with A, I, L, S, T, M, or V; S168 replaced with A, G, I, L, T, M, or V; T169 replaced with A, G, I, L, S, M, or V; V170 replaced with A, G, I, L, S, T, or M; K171 replaced with H, or R; E172 replaced with D; D173 replaced with E; N174 replaced with Q; G176 replaced with A, I, L, S, T, M, or V; V 177 replaced with A, G, I, L, S, T, or M; N179 replaced with Q; G180 replaced with A, I, L, S, T, M, or V; D181 replaced with E; G182 replaced with A, I, L, S, T, M, or V; S183 replaced with A, G, I, L, T, M, or V; T184 replaced with A, G, I, L, S, M, or V; R186 replaced with H, or K; L187 replaced with A, G, I, S, T, M, or V; V188 replaced with A, G, I, L, S, T, or M; R189 replaced with H, or K; G190 replaced with A, I, L, S, T, M, or V; Q191 replaced with N; Y192 replaced with F, or W; K193 replaced with H, or R; S194 replaced with A, G, I, L, T, M, or V; Q195 replaced with N; L196 replaced with A, G, I, S, T, M, or V; S197 replaced with A, G, I, L, T, M, or V; A198 replaced with G, I, L, S, T, M, or V; T199 replaced with A, G, I, L, S, M, or V; K200 replaced with H, or R; S201 replaced with A, G, I, L, T, M, or V; D202 replaced with E; D203 replaced with E; T204 replaced with A, G, I, L, S, M, or V; V205 replaced with A, G, I, L, S, T, or M; V206 replaced with A, G, I, L, S, T, or M; A207 replaced with G, I, L, S, T, M, or V; I208 replaced with A, G, L, S, T, M, or V; Y210 replaced with F, or W; G211 replaced with A, I, L, S, T, M, or V; S212 replaced with A, G, I, L, T, M, or V; R213 replaced with H, or K; H214 replaced with K, or R; I215 replaced with A, G, L, S, T, M, or V; R216 replaced with H, or K; L217 replaced with A, G, I, S, T, M, or V; V218 replaced with A, G, I, L, S, T, or M; L219 replaced with A, G, I, S, T, M, or V; K220 replaced with H, or R; G221 replaced with A, I, L, S, T, M, or V; D223 replaced with E; H224 replaced with K, or R; L225 replaced with A, G, I, S, T, M, or V; Y226 replaced with F, or W; L227 replaced with A, G, I, S, T, M, or V; E228 replaced with D; T229 replaced with A, G, I, L, S, M, or V; K230 replaced with H, or R; T231 replaced with A, G, I, L, S, M, or V; L232 replaced with A, G, I, S, T, M, or V; Q233 replaced with N; G234 replaced with A, I, L, S, T, M, or V; T235 replaced with A, G, I, L, S, M, or V; K236 replaced with H, or R; G237 replaced with A, I, L, S, T, M, or V; E238 replaced with D; N239 replaced with Q; S240 replaced with A, G, I, L, T, M, or V; L241 replaced with A, G, I, S, T, M, or V; S242 replaced with A, G, I, L, T, M, or V; S243 replaced with A, G, I, L, T, M, or V; T244 replaced with A, G, I, L, S, M, or V; G245 replaced with A, I, L, S, T, M, or V; T246 replaced with A, G, I, L, S, M, or V; F247 replaced with W, or Y; L248 replaced with A, G, I, S, T, M, or V; V249 replaced with A, G, I, L, S, T, or M; D250 replaced with E; N251 replaced with Q; S252 replaced with A, G, I, L, T, M, or V; S253 replaced with A, G, I, L, T, M, or V; V254 replaced with A, G, I, L, S, T, or M; D255 replaced with E; F256 replaced with W, or Y; Q257 replaced with N; K258 replaced with H, or R; F259 replaced with W, or Y; D261 replaced with E; K262 replaced with H, or R; E263 replaced with D; I264 replaced with A, G, L, S, T, M, or V; L265 replaced with A, G, I, S, T, M, or V; R266 replaced with H, or K; M267 replaced with A, G, I, L, S, T, or V; A268 replaced with G, I, L, S, T, M, or V; G269 replaced with A, I, L, S, T, M, or V; L271 replaced with A, G, I, S, T, M, or V; T272 replaced with A, G, I, L, S, M, or V; A273 replaced with G, I, L, S, T, M, or V; D274 replaced with E; F275 replaced with W, or Y; I276 replaced with A, G, L, S, T, M, or V; V277 replaced with A, G, I, L, S, T, or M; K278 replaced with H, or R; I279 replaced with A, G, L, S, T, M, or V; R280 replaced with H, or K; N281 replaced with Q; S282 replaced with A, G, I, L, T, M, or V; G283 replaced with A, I, L, S, T, M, or V; S284 replaced with A, G, I, L, T, M, or V; A285 replaced with G, I, L, S, T, M, or V; D286 replaced with E; S287 replaced with A, G, I, L, T, M, or V; T288 replaced with A, G, I, L, S, M, or V; V289 replaced with A, G, I, L, S, T, or M; Q290 replaced with N; F291 replaced with W, or Y; I292 replaced with A, G, L, S, T, M, or V; F293 replaced with W, or Y; Y294 replaced with F, or W; Q295 replaced with N; I297 replaced with A, G, L, S, T, M, or V; I298 replaced with A, G, L, S, T, M, or V; H299 replaced with K, or R; R300 replaced with H, or K; W301 replaced with F, or Y; R302 replaced with H, or K; E303 replaced with D; T304 replaced with A, G, I, L, S, M, or V; D305 replaced with E; F306 replaced with W, or Y; F307 replaced with W, or Y; S310 replaced with A, G, I, L, T, M, or V; A311 replaced with G, I, L, S, T, M, or V; T312 replaced with A, G, I, L, S, M, or V; G314 replaced with A, I, L, S, T, M, or V; G315 replaced with A, I, L, S, T, M, or V; G316 replaced with A, I, L, S, T, M, or V; Y317 replaced with F, or W; Q318 replaced with N; L319 replaced with A, G, I, S, T, M, or V; T320 replaced with A, G, I, L, S, M, or V; S321 replaced with A, G, I, L, T, M, or V; A322 replaced with G, I, L, S, T, M, or V; E323 replaced with D; Y325 replaced with F, or W; D326 replaced with E; L327 replaced with A, G, I, S, T, M, or V; R328 replaced with H, or K; S329 replaced with A, G, I, L, T, M, or V; N330 replaced with Q; R331 replaced with H, or K; V332 replaced with A, G, I, L, S, T, or M; V333 replaced with A, G, I, L, S, T, or M; A334 replaced with G, I, L, S, T, M, or V; D335 replaced with E; Q336 replaced with N; Y337 replaced with F, or W; H339 replaced with K, or R; Y340 replaced with F, or W; Y341 replaced with F, or W; E343 replaced with D; N344 replaced with Q; I345 replaced with A, G, L, S, T, M, or V; K346 replaced with H, or R; K348 replaced with H, or R; K350 replaced with H, or R; L351 replaced with A, G, I, S, T, M, or V; Q352 replaced with N; E353 replaced with D; N355 replaced with Q; L356 replaced with A, G, I, S, T, M, or V; D357 replaced with E; A361 replaced with G, I, L, S, T, M, or V; R362 replaced with H, or K; W363 replaced with F, or Y; E364 replaced with D; A365 replaced with G, I, L, S, T, M, or V; T366 replaced with A, G, I, L, S, M, or V; W368 replaced with F, or Y; T369 replaced with A, G, I, L, S, M, or V; A370 replaced with G, I, L, S, T, M, or V; S372 replaced with A, G, I, L, T, M, or V; S373 replaced with A, G, I, L, T, M, or V; S374 replaced with A, G, I, L, T, M, or V; G376 replaced with A, I, L, S, T, M, or V; G377 replaced with A, G, L, S, T, M, or V; G378 replaced with A, I, L, S, T, M, or V; I379 replaced with A, G, L, S, T, M, or V; Q380 replaced with N; S381 replaced with A, G, I, L, T, M, or V; R382 replaced with H, or K; A383 replaced with G, I, L, S, T, M, or V; V384 replaced with A, G, I, L, S, T, or M; S385 replaced with A, G, I, L, T, M, or V; V387 replaced with A, G, I, L, S, T, or M; E388 replaced with D; E389 replaced with D; D390 replaced with E; I391 replaced with A, G, L, S, T, M, or V; Q392 replaced with N; G393 replaced with A, I, L, S, T, M, or V; H394 replaced with K, or R; V395 replaced with A, G, I, L, S, T, or M; T396 replaced with A, G, I, L, S, M, or V; S397 replaced with A, G, I, L, T, M, or V; V398 replaced with A, G, I, L, S, T, or M; E399 replaced with D; E400 replaced with D; W401 replaced with F, or Y; K402 replaced with H, or R; M404 replaced with A, G, I, L, S, T, or V; Y405 replaced with F, or W; T406 replaced with A, G, I, L, S, M, or V; K408 replaced with H, or R; M409 replaced with A, G, I, L, S, T, or V; I411 replaced with A, G, L, S, T, M, or V; A412 replaced with G, I, L, S, T, M, or V; Q413 replaced with N; N416 replaced with Q; I417 replaced with A, G, L, S, T, M, or V; F418 replaced with W, or Y; D419 replaced with E; K422 replaced with H, or R; W423 replaced with F, or Y; L424 replaced with A, G, I, S, T, M, or V; A425 replaced with G, I, L, S, T, M, or V; Q426 replaced with N; E427 replaced with D; W428 replaced with F, or Y; S429 replaced with A, G, I, L, T, M, or V; T432 replaced with A, G, I, L, S, M, or V; V433 replaced with A, G, I, L, S, T, or M; T434 replaced with A, G, I, L, S, M, or V; G436 replaced with A, I, L, S, T, M, or V; Q437 replaced with N; G438 replaced with A, I, L, S, T, M, or V; L439 replaced with A, G, I, S, T, M, or V; R440 replaced with H, or K; Y441 replaced with F, or W; R442 replaced with H, or K; V443 replaced with A, G, I, L, S, T, or M; V444 replaced with A, G, I, L, S, T, or M; L445 replaced with A, G, I, S, T, M, or V; I447 replaced with A, G, L, S, T, M, or V; D448 replaced with E; H449 replaced with K, or R; R450 replaced with H, or K; G451 replaced with A, I, L, S, T, M, or V; M452 replaced with A, G, I, L, S, T, or V; H453 replaced with K, or R; T454 replaced with A, G, I, L, S, M, or V; G455 replaced with A, I, L, S, T, M, or V; G456 replaced with A, I, L, S, T, M, or V; S458 replaced with A, G, I, L, T, M, or V; K460 replaced with H, or R; T461 replaced with A, G, I, L, S, M, or V; K462 replaced with H, or R; H464 replaced with K, or R; I465 replaced with A, G, L, S, T, M, or V; K466 replaced with H, or R; E467 replaced with D; E468 replaced with D; I470 replaced with A, G, L, S, T, M, or V; V471 replaced with A, G, I, L, S, T, or M; T473 replaced with A, G, I, L, S, M, or V; Y476 replaced with F, or W; K477 replaced with H, or R; K479 replaced with H, or R; E480 replaced with D; K481 replaced with H, or R; L482 replaced with A, G, I, S, T, M, or V; V484 replaced with A, G, I, L, S, T, or M; E485 replaced with D; A486 replaced with G, I, L, S, T, M, or V; K487 replaced with H, or R; L488 replaced with A, G, I, S, T, M, or V; W490 replaced with F, or Y; F491 replaced with W, or Y; K492 replaced with H, or R; Q493 replaced with N; A494 replaced with G, I, L, S, T, M, or V; Q495 replaced with N; E496 replaced with D; L497 replaced with A, G, I, S, T, M, or V; E498 replaced with D; E499 replaced with D; G500 replaced with A, I, L, S, T, M, or V; A501 replaced with G, I, L, S, T, M, or V; A502 replaced with G, I, L, S, T, M, or V; V503 replaced with A, G, I, L, S, T, or M; S504 replaced with A, G, I, L, T, M, or V; E505 replaced with D; E506 replaced with D; S508 replaced with A, G, I, L, T, M, or V; F509 replaced with W, or Y; I510 replaced with A, G, L, S, T, M, or V; K512 replaced with H, or R; A513 replaced with G, I, L, S, T, M, or V; W514 replaced with F, or Y; S515 replaced with A, G, I, L, T, M, or V; A516 replaced with G, I, L, S, T, M, or V; T518 replaced with A, G, I, L, S, M, or V; V519 replaced with A, G, I, L, S, T, or M; T520 replaced with A, G, I, L, S, M, or V; G522 replaced with A, I, L, S, T, M, or V; V523 replaced with A, G, I, L, S, T, or M; G524 replaced with A, I, L, S, T, M, or V; T525 replaced with A, G, I, L, S, M, or V; Q526 replaced with N; V527 replaced with A, G, I, L, S, T, or M; R528 replaced with H, or K; I529 replaced with A, G, L, S, T, M, or V; V530 replaced with A, G, I, L, S, T, or M; R531 replaced with H, or K; Q533 replaced with N; V534 replaced with A, G, I, L, S, T, or M; L535 replaced with A, G, I, S, T, M, or V; L536 replaced with A, G, I, S, T, M, or V; S537 replaced with A, G, I, L, T, M, or V; F538 replaced with W, or Y; S539 replaced with A, G, I, L, T, M, or V; Q540 replaced with N; S541 replaced with A, G, I, L, T, M, or V; V542 replaced with A, G, I, L, S, T, or M; A543 replaced with G, I, L, S, T, M, or V; D544 replaced with E; L545 replaced with A, G, I, S, T, M, or V; I547 replaced with A, G, L, S, T, M, or V; D548 replaced with E; E549 replaced with D; E551 replaced with D; G552 replaced with A, I, L, S, T, M, or V; K554 replaced with H, or R; A556 replaced with G, I, L, S, T, M, or V; S557 replaced with A, G, I, L, T, M, or V; Q558 replaced with N; R559 replaced with H, or K; A560 replaced with G, I, L, S, T, M, or V; Y562 replaced with F, or W; A563 replaced with G, I, L, S, T, M, or V; G564 replaced with A, I, L, S, T, M, or V; S567 replaced with A, G, I, L, T, M, or V; G568 replaced with A, I, L, S, T, M, or V; E569 replaced with D; I570 replaced with A, G, L, S, T, M, or V; E572 replaced with D; F573 replaced with W, or Y; N574 replaced with Q; D576 replaced with E; E577 replaced with D; T578 replaced with A, G, I, L, S, M, or V; D579 replaced with E; G580 replaced with A, I, L, S, T, M, or V; L581 replaced with A, G, I, S, T, M, or V; F582 replaced with W, or Y; G583 replaced with A, I, L, S, T, M, or V; G584 replaced with A, I, L, S, T, M, or V; L585 replaced with A, G, I, S, T, M, or V; Q586 replaced with N; D587 replaced with E; F588 replaced with W, or Y; D589 replaced with E; E590 replaced with D; L591 replaced with A, G, I, S, T, M, or V; Y592 replaced with F, or W; D593 replaced with E; W594 replaced with F, or Y; E595 replaced with D; Y596 replaced with F, or W; E597 replaced with D; G598 replaced with A, I, L, S, T, M, or V; F599 replaced with W, or Y; T600 replaced with A, G, I, L, S, M, or V; K601 replaced with H, or R; S603 replaced with A, G, I, L, T, M, or V; E604 replaced with D; S605 replaced with A, G, I, L, T, M, or V; G607 replaced with A, I, L, S, T, M, or V; G608 replaced with A, I, L, S, T, M, or V; G609 replaced with A, I, L, S, T, M, or V; V610 replaced with A, G, I, L, S, T, or M; Q611 replaced with N; E612 replaced with D; A613 replaced with G, I, L, S, T, M, or V; V614 replaced with A, G, I, L, S, T, or M; V615 replaced with A, G, I, L, S, T, or M; S616 replaced with A, G, I, L, T, M, or V; L618 replaced with A, G, I, S, T, M, or V; N619 replaced with Q; K620 replaced with H, or R; Q621 replaced with N; T622 replaced with A, G, I, L, S, M, or V; R623 replaced with H, or K; E624 replaced with D; A626 replaced with G, I, L, S, T, M, or V; E627 replaced with D; E628 replaced with D; N629 replaced with Q; L630 replaced with A, G, I, S, T, M, or V; V632 replaced with A, G, I, L, S, T, or M; T633 replaced with A, G, I, L, S, M, or V; S634 replaced with A, G, I, L, T, M, or V; R635 replaced with H, or K; R636 replaced with H, or K; Q639 replaced with N; L640 replaced with A, G, I, S, T, M, or V; L641 replaced with A, G, I, S, T, M, or V; K642 replaced with H, or R; S643 replaced with A, G, I, L, T, M, or V; N645 replaced with Q; L646 replaced with A, G, I, S, T, M, or V; D647 replaced with E; A651 replaced with G, I, L, S, T, M, or V; R652 replaced with H, or K; W653 replaced with F, or Y; E654 replaced with D; I655 replaced with A, G, L, S, T, M, or V; G656 replaced with A, I, L, S, T, M, or V; K657 replaced with H, or R; W658 replaced with F, or Y; S659 replaced with A, G, I, L, T, M, or V; S662 replaced with A, G, I, L, T, M, or V; L663 replaced with A, G, I, S, T, M, or V; T664 replaced with A, G, I, L, S, M, or V; G666 replaced with A, I, L, S, T, M, or V; V667 replaced with A, G, I, L, S, T, or M; G668 replaced with A, I, L, S, T, M, or V; L669 replaced with A, G, I, S, T, M, or V; Q670 replaced with N; T671 replaced with A, G, I, L, S, M, or V; R672 replaced with H, or K; D673 replaced with E; V674 replaced with A, G, I, L, S, T, or M; F675 replaced with W, or Y; S677 replaced with A, G, I, L, T, M, or V; H678 replaced with K, or R; L679 replaced with A, G, I, S, T, M, or V; L680 replaced with A, G, I, S, T, M, or V; S681 replaced with A, G, I, L, T, M, or V; R682 replaced with H, or K; E683 replaced with D; M684 replaced with A, G, I, L, S, T, or V; N685 replaced with Q; E686 replaced with D; T687 replaced with A, G, I, L, S, M, or V; V688 replaced with A, G, I, L, S, T, or M; I689 replaced with A, G, L, S, T, M, or V; L690 replaced with A, G, I, S, T, M, or V; A691 replaced with G, I, L, S, T, M, or V; D692 replaced with E; E693 replaced with D; L694 replaced with A, G, I, S, T, M, or V; R696 replaced with H, or K; Q697 replaced with N; K699 replaced with H, or R; S701 replaced with A, G, I, L, T, M, or V; T702 replaced with A, G, I, L, S, M, or V; V703 replaced with A, G, I, L, S, T, or M; Q704 replaced with N; A705 replaced with G, I, L, S, T, M, or V; N707 replaced with Q; R708 replaced with H, or K; F709 replaced with W, or Y; N710 replaced with Q; A714 replaced with G, I, L, S, T, M, or V; W715 replaced with F, or Y; Y716 replaced with F, or W; A718 replaced with G, I, L, S, T, M, or V; Q719 replaced with N; W720 replaced with F, or Y; Q721 replaced with N; S724 replaced with A, G, I, L, T, M, or V; R725 replaced with H, or K; T726 replaced with A, G, I, L, S, M, or V; G728 replaced with A, I, L, S, T, M, or V; G729 replaced with A, I, L, S, T, M, or V; G730 replaced with A, I, L, S, T, M, or V; V731 replaced with A, G, I, L, S, T, or M; Q732 replaced with N; K733 replaced with H, or R; R734 replaced with H, or K; E735 replaced with D; V736 replaced with A, G, I, L, S, T, or M; L737 replaced with A, G, I, S, T, M, or V; K739 replaced with H, or R; Q740 replaced with N; R741 replaced with H, or K; M742 replaced with A, G, I, L, S, T, or V; A743 replaced with G, I, L, S, T, M, or V; D744 replaced with E; G745 replaced with A, I, L, S, T, M, or V; S746 replaced with A, G, I, L, T, M, or V; F747 replaced with W, or Y; L748 replaced with A, G, I, S, T, M, or V; E749 replaced with D; L750 replaced with A, G, I, S, T, M, or V; E752 replaced with D; T753 replaced with A, G, I, L, S, M, or V; F754 replaced with W, or Y; S756 replaced with A, G, I, L, T, M, or V; A757 replaced with G, I, L, S, T, M, or V; S758 replaced with A, G, I, L, T, M, or V; K759 replaced with H, or R; A761 replaced with G, I, L, S, T, M, or V; Q763 replaced with N; Q764 replaced with N; A765 replaced with G, I, L, S, T, M, or V; K767 replaced with H, or R; K768 replaced with H, or R; D769 replaced with E; D770 replaced with E; S773 replaced with A, G, I, L, T, M, or V; E774 replaced with D; W775 replaced with F, or Y; L776 replaced with A, G, I, S, T, M, or V; L777 replaced with A, G, I, S, T, M, or V; S778 replaced with A, G, I, L, T, M, or V; D779 replaced with E; W780 replaced with F, or Y; T781 replaced with A, G, I, L, S, M, or V; E782 replaced with D; S784 replaced with A, G, I, L, T, M, or V; T785 replaced with A, G, I, L, S, M, or V; S786 replaced with A, G, I, L, T, M, or V; G788 replaced with A, I, L, S, T, M, or V; E789 replaced with D; G790 replaced with A, I, L, S, T, M, or V; T791 replaced with A, G, I, L, S, M, or V; Q792 replaced with N; T793 replaced with A, G, I, L, S, M, or V; R794 replaced with H, or K; S795 replaced with A, G, I, L, T, M, or V; A796 replaced with G, I, L, S, T, M, or V; I797 replaced with A, G, L, S, T, M, or V; R799 replaced with H, or K; K800 replaced with H, or R. M801 replaced with A, G, I, L, S, T, or V; L802 replaced with A, G, I, S, T, M, or V; K803 replaced with H, or R; T804 replaced with A, G, I, L, S, M, or V; G805 replaced with A, I, L, S, T, M, or V; L806 replaced with A, G, I, S, T, M, or V; S807 replaced with A, G, I, L, T, M, or V; T808 replaced with A, G, I, L, S, M, or V; V809 replaced with A, G, I, L, S, T, or M; V810 replaced with A, G, I, L, S, T, or M; N811 replaced with Q; S812 replaced with A, G, I, L, T, M, or V; T813 replaced with A, G, I, L, S, M, or V; L814 replaced with A, G, I, S, T, M, or V; L818 replaced with A, G, I, S, T, M, or V; F820 replaced with W, or Y; S821 replaced with A, G, I, L, T, M, or V; S822 replaced with A, G, I, L, T, M, or V; S823 replaced with A, G, I, L, T, M, or V; I824 replaced with A, G, L, S, T, M, or V; R825 replaced with H, or K; M828 replaced with A, G, I, L, S, T, or V; L829 replaced with A, G, I, S, T, M, or V; A830 replaced with G, I, L, S, T, M, or V; T831 replaced with A, G, I, L, S, M, or V; A833 replaced with G, I, L, S, T, M, or V; R834 replaced with H, or K; G836 replaced with A, I, L, S, T, M, or V; R837 replaced with H, or K; S839 replaced with A, G, I, L, T, M, or V; T840 replaced with A, G, I, L, S, M, or V; K841 replaced with H, or R; H842 replaced with K, or R; S843 replaced with A, G, I, L, T, M, or V; H845 replaced with K, or R; I846 replaced with A, G, L, S, T, M, or V; A847 replaced with G, I, L, S, T, M, or V; A848 replaced with G, I, L, S, T, M, or V; A849 replaced with G, I, L, S, T, M, or V; R850 replaced with H, or K; K851 replaced with H, or R; V852 replaced with A, G, I, L, S, T, or M; Y853 replaced with F, or W; I854 replaced with A, G, L, S, T, M, or V; Q855 replaced with N; T856 replaced with A, G, I, L, S, M, or V; R857 replaced with H, or K; R858 replaced with H, or K; Q859 replaced with N; R860 replaced with H, or K; K861 replaced with H, or R; L862 replaced with A, G, I, S, T, M, or V; H863 replaced with K, or R; F864 replaced with W, or Y; V865 replaced with A, G, I, L, S, T, or M; V866 replaced with A, G, I, L, S, T, or M; G867 replaced with A, I, L, S, T, M, or V; G868 replaced with A, I, L, S, T, M, or V; F869 replaced with W, or Y; A870 replaced with G, I, L, S, T, M, or V; Y871 replaced with F, or W; L872 replaced with A, G, I, S, T, M, or V; L873 replaced with A, G, I, S, T, M, or V; K875 replaced with H, or R; T876 replaced with A, G, I, L, S, M, or V; A877 replaced with G, I, L, S, T, M, or V; V878 replaced with A, G, I, L, S, T, or M; V879 replaced with A, G, I, L, S, T, or M; L880 replaced with A, G, I, S, T, M, or V; R881 replaced with H, or K; A884 replaced with G, I, L, S, T, M, or V; R885 replaced with H, or K; R886 replaced with H, or K; V887 replaced with A, G, I, L, S, T, or M; R888 replaced with H, or K; K889 replaced with H, or R; L891 replaced with A, G, I, S, T, M, or V; I892 replaced with A, G, L, S, T, M, or V; T893 replaced with A, G, I, L, S, M, or V; W894 replaced with F, or Y; E895 replaced with D; K896 replaced with H, or R; D897 replaced with E; G898 replaced with A, I, L, S, T, M, or V; Q899 replaced with N; H900 replaced with K, or R; L901 replaced with A, G, I, S, T, M, or V; I902 replaced with A, G, L, S, T, M, or V; S903 replaced with A, G, I, L, T, M, or V; S904 replaced with A, G, I, L, T, M, or V; T905 replaced with A, G, I, L, S, M, or V; H906 replaced with K, or R; V907 replaced with A, G, I, L, S, T, or M; T908 replaced with A, G, I, L, S, M, or V; V909 replaced with A, G, I, L, S, T, or M; A910 replaced with G, I, L, S, T, M, or V; F912 replaced with W, or Y; G913 replaced with A, I, L, S, T, M, or V; Y914 replaced with F, or W; L915 replaced with A, G, I, S, T, M, or V; K916 replaced with H, or R; I917 replaced with A, G, L, S, T, M, or V; H918 replaced with K, or R; R919 replaced with H, or K; L920 replaced with A, G, I, S, T, M, or V; K921 replaced with H, or R; S923 replaced with A, G, I, L, T, M, or V; D924 replaced with E; A925 replaced with G, I, L, S, T, M, or V; G926 replaced with A, I, L, S, T, M, or V; V927 replaced with A, G, I, L, S, T, or M; Y928 replaced with F, or W; T929 replaced with A, G, I, L, S, M, or V; S931 replaced with A, G, I, L, T, M, or V; A932 replaced with G, I, L, S, T, M, or V; G933 replaced with A, I, L, S, T, M, or V; A935 replaced with G, I, L, S, T, M, or V; R936 replaced with H, or K; E937 replaced with D; H938 replaced with K, or R; F939 replaced with W, or Y; V940 replaced with A, G, I, L, S, T, or M; I941 replaced with A, G, L, S, T, M, or V; K942 replaced with H, or R; L943 replaced with A, G, I, S, T, M, or V; I944 replaced with A, G, L, S, T, M, or V; G945 replaced with A, I, L, S, T, M, or V; G946 replaced with A, I, L, S, T, M, or V; N947 replaced with Q; R948 replaced with H, or K; K949 replaced with H, or R; L950 replaced with A, G, I, S, T, M, or V; V951 replaced with A, G, I, L, S, T, or M; A952 replaced with G, I, L, S, T, M, or V; R953 replaced with H, or K; L955 replaced with A, G, I, S, T, M, or V; S956 replaced with A, G, I, L, T, M, or V; R958 replaced with H, or K; S959 replaced with A, G, I, L, T, M, or V; E960 replaced with D; E961 replaced with D; E962 replaced with D; V963 replaced with A, G, I, L, S, T, or M; L964 replaced with A, G, I, S, T, M, or V; A965 replaced with G, I, L, S, T, M, or V; G966 replaced with A, I, L, S, T, M, or V; R967 replaced with H, or K; K968 replaced with H, or R; G969 replaced with A, I, L, S, T, M, or V; G970 replaced with A, I, L, S, T, M, or V; K972 replaced with H, or R; E973 replaced with D; A974 replaced with G, I, L, S, T, M, or V; L975 replaced with A, G, I, S, T, M, or V; Q976 replaced with N; T977 replaced with A, G, I, L, S, M, or V; H978 replaced with K, or R; K979 replaced with H, or R; H980 replaced with K, or R; Q981 replaced with N; N982 replaced with Q; G983 replaced with A, I, L, S, T, M, or V; I984 replaced with A, G, L, S, T, M, or V; F985 replaced with W, or Y; S986 replaced with A, G, I, L, T, M, or V; N987 replaced with Q; G988 replaced with A, I, L, S, T, M, or V; S989 replaced with A, G, I, L, T, M, or V; K990 replaced with H, or R; A991 replaced with G, I, L, S, T, M, or V; E992 replaced with D; K993 replaced with H, or R; R994 replaced with H, or K; G995 replaced with A, I, L, S, T, M, or V; L996 replaced with A, G, I, S, T, M, or V; A997 replaced with G, I, L, S, T, M, or V; A998 replaced with G, I, L, S, T, M, or V; N999 replaced with Q; G1001 replaced with A, I, L, S, T, M, or V; S1002 replaced with A, G, I, L, T, M, or V; R1003 replaced with H, or K; Y1004 replaced with F, or W; D1005 replaced with E; D1006 replaced with E; L 1007 replaced with A, G, I, S, T, M, or V; V1008 replaced with A, G, I, L, S, T, or M; S1009 replaced with A, G, I, L, T, M, or V; R1010 replaced with H, or K; L1011 replaced with A, G, I, S, T, M, or V; L1012 replaced with A, G, I, S, T, M, or V; E1013 replaced with D; Q1014 replaced with N; G1015 replaced with A, I, L, S, T, M, or V; G1016 replaced with A, I, L, S, T, M, or V; W1017 replaced with F, or Y; G1019 replaced with A, I, L, S, T, M, or V; E1020 replaced with D; L1021 replaced with A, G, I, S, T, M, or V; L1022 replaced with A, G, I, S, T, M, or V; A1023 replaced with G, I, L, S, T, M, or V; S1024 replaced with A, G, I, L, T, M, or V; W1025 replaced with F, or Y; E1026 replaced with D; A1027 replaced with G, I, L, S, T, M, or V; Q1028 replaced with N; D1029 replaced with E; S1030 replaced with A, G, I, L, T, M, or V; A1031 replaced with G, I, L, S, T, M, or V; E1032 replaced with D; R1033 replaced with H, or K; N1034 replaced with Q; T1035 replaced with A, G, I, L, S, M, or V; T1036 replaced with A, G, I, L, S, M, or V; S1037 replaced with A, G, I, L, T, M, or V; E1038 replaced with D; E1039 replaced with D; D1040 replaced with E; G1042 replaced with A, I, L, S, T, M, or V; A1043 replaced with G, I, L, S, T, M, or V; E1044 replaced with D; Q1045 replaced with N; V1046 replaced with A, G, I, L, S, T, or M; L1047 replaced with A, G, I, S, T, M, or V; L1048 replaced with A, G, I, S, T, M, or V; H1049 replaced with K, or R; L1050 replaced with A, G, I, S, T, M, or V; F1052 replaced with W, or Y; T1053 replaced with A, G, I, L, S, M, or V; M1054 replaced with A, G, I, L, S, T, or V; V 1055 replaced with A, G, I, L, S, T, or M; T1056 replaced with A, G, I, L, S, M, or V; E1057 replaced with D; Q1058 replaced with N; R1059 replaced with H, or K; R1060 replaced with H, or K; L1061 replaced with A, G, I, S, T, M, or V; D1062 replaced with E; D1063 replaced with E; I1064 replaced with A, G, L, S, T, M, or V; L1065 replaced with A, G, I, S, T, M, or V; G1066 replaced with A, I, L, S, T, M, or V; N1067 replaced with Q; L1068 replaced with A, G, I, S, T, M, or V; S1069 replaced with A, G, I, L, T, M, or V; Q1070 replaced with N; Q1071 replaced with N; E1073 replaced with D; E1074 replaced with D; L1075 replaced with A, G, I, S, T, M, or V; R1076 replaced with H, or K; D1077 replaced with E; L1078 replaced with A, G, I, S, T, M, or V; Y1079 replaced with F, or W; S1080 replaced with A, G, I, L, T, M, or V; K1081 replaced with H, or R; H1082 replaced with K, or R; L1083 replaced with A, G, I, S, T, M, or V; V1084 replaced with A, G, I, L, S, T, or M; A1085 replaced with G, I, L, S, T, M, or V; Q1086 replaced with N; L1087 replaced with A, G, I, S, T, M, or V; A1088 replaced with G, I, L, S, T, M, or V; Q1089 replaced with N; E1090 replaced with D; I1091 replaced with A, G, L, S, T, M, or V; F1092 replaced with W, or Y; R1093 replaced with H, or K; S1094 replaced with A, G, I, L, T, M, or V; H1095 replaced with K, or R; L1096 replaced with A, G, I, S, T, M, or V; E1097 replaced with D; H1098 replaced with K, or R; Q1099 replaced with N; D1100 replaced with E; T1101 replaced with A, G, I, L, S, M, or V; L1102 replaced with A, G, I, S, T, M, or V; L1103 replaced with A, G, I, S, T, M, or V; K1104 replaced with H, or R; S1106 replaced with A, G, I, L, T, M, or V; E1107 replaced with D; R1108 replaced with H, or K; R 1109 replaced with H, or K; T1110 replaced with A, G, I, L, S, M, or V; S1111 replaced with A, G, I, L, T, M, or V; V1113 replaced with A, G, I, L, S, T, or M; T1114 replaced with A, G, I, L, S, M, or V; L1115 replaced with A, G, I, S, T, M, or V; S1116 replaced with A, G, I, L, T, M, or V; H1118 replaced with K, or R; K1119 replaced with H, or R; H1120 replaced with K, or R; V1121 replaced with A, G, I, L, S, T, or M; S1122 replaced with A, G, I, L, T, M, or V; G1123 replaced with A, I, L, S, T, M, or V; F1124 replaced with W, or Y; S1125 replaced with A, G, I, L, T, M, or V; S1126 replaced with A, G, I, L, T, M, or V; S1127 replaced with A, G, I, L, T, M, or V; L1128 replaced with A, G, I, S, T, M, or V; R1129 replaced with H, or K; T1130 replaced with A, G, I, L, S, M, or V; S1131 replaced with A, G, I, L, T, M, or V; S1132 replaced with A, G, I, L, T, M, or V; T1133 replaced with A, G, I, L, S, M, or V; G1134 replaced with A, I, L, S, T, M, or V; D1135 replaced with E; A1136 replaced with G, I, L, S, T, M, or V; G1137 replaced with A, I, L, S, T, M, or V; G1138 replaced with A, I, L, S, T, M, or V; G1139 replaced with A, I, L, S, T, M, or V; S1140 replaced with A, G, I, L, T, M, or V; R1141 replaced with H, or K; R1142 replaced with H, or K; H1144 replaced with K, or R; R1145 replaced with H, or K; K1146 replaced with H, or R; T1148 replaced with A, G, I, L, S, M, or V; I1149 replaced with A, G, L, S, T, M, or V; L1150 replaced with A, G, I, S, T, M, or V; R1151 replaced with H, or K; K1152 replaced with H, or R; I1153 replaced with A, G, L, S, T, M, or V; S1154 replaced with A, G, I, L, T, M, or V; A1155 replaced with G, I, L, S, T, M, or V; A1156 replaced with G, I, L, S, T, M, or V; Q1157 replaced with N; Q1158 replaced with N; L1159 replaced with A, G, I, S, T, M, or V; S1160 replaced with A, G, I, L, T, M, or V; A1161 replaced with G, I, L, S, T, M, or V; S1162 replaced with A, G, I, L, T, M, or V; E1163 replaced with D; V1164 replaced with A, G, I, L, S, T, or M; V1165 replaced with A, G, I, L, S, T, or M; T1166 replaced with A, G, I, L, S, M, or V; H1167 replaced with K, or R; L1168 replaced with A, G, I, S, T, M, or V; G1169 replaced with A, I, L, S, T, M, or V; Q1170 replaced with N; T1171 replaced with A, G, I, L, S, M, or V; V1172 replaced with A, G, I, L, S, T, or M; A1173 replaced with G, I, L, S, T, M, or V; L1174 replaced with A, G, I, S, T, M, or V; A1175 replaced with G, I, L, S, T, M, or V; S1176 replaced with A, G, I, L, T, M, or V; G1177 replaced with A, I, L, S, T, M, or V; T1178 replaced with A, G, I, L, S, M, or V; L1179 replaced with A, G, I, S, T, M, or V; S1180 replaced with A, G, I, L, T, M, or V; V 1181 replaced with A, G, I, L, S, T, or M; L1182 replaced with A, G, I, S, T, M, or V; L1183 replaced with A, G, I, S, T, M, or V; H1184 replaced with K, or R; E1186 replaced with D; A1187 replaced with G, I, L, S, T, M, or V; I1188 replaced with A, G, L, S, T, M, or V; G1189 replaced with A, I, L, S, T, M, or V; H1190 replaced with K, or R; R1192 replaced with H, or K; T1194 replaced with A, G, I, L, S, M, or V; I1195 replaced with A, G, L, S, T, M, or V; S1196 replaced with A, G, I, L, T, M, or V; W1197 replaced with F, or Y; A1198 replaced with G, I, L, S, T, M, or V; R1199 replaced with H, or K; N1200 replaced with Q; G1201 replaced with A, I, L, S, T, M, or V; E1202 replaced with D; E1203 replaced with D; V1204 replaced with A, G, I, L, S, T, or M; Q1205 replaced with N; F1206 replaced with W, or Y; S1207 replaced with A, G, I, L, T, M, or V; D1208 replaced with E; R1209 replaced with H, or K; I1210 replaced with A, G, L, S, T, M, or V; L1211 replaced with A, G, I, S, T, M, or V; L1212 replaced with A, G, I, S, T, M, or V; Q1213 replaced with N; D1215 replaced with E; D1216 replaced with E; S1217 replaced with A, G, I, L, T, M, or V; L1218 replaced with A, G, I, S, T, M, or V; Q1219 replaced with N; I1220 replaced with A, G, L, S, T, M, or V; L1221 replaced with A, G, I, S, T, M, or V; A1222 replaced with G, I, L, S, T, M, or V; V1224 replaced with A, G, I, L, S, T, or M; E1225 replaced with D; A1226 replaced with G, I, L, S, T, M, or V; D1227 replaced with E; V1228 replaced with A, G, I, L, S, T, or M; G1229 replaced with A, I, L, S, T, M, or V; F1230 replaced with W, or Y; Y1231 replaced with F, or W; T1232 replaced with A, G, I, L, S, M, or V; N1234 replaced with Q; A1235 replaced with G, I, L, S, T, M, or V; T1236 replaced with A, G, I, L, S, M, or V; N1237 replaced with Q; A1238 replaced with G, I, L, S, T, M, or V; L1239 replaced with A, G, I, S, T, M, or V; G1240 replaced with A, I, L, S, T, M, or V; Y1241 replaced with F, or W; D1242 replaced with E; S1243 replaced with A, G, I, L, T, M, or V; V1244 replaced with A, G, I, L, S, T, or M; S1245 replaced with A, G, I, L, T, M, or V; I1246 replaced with A, G, L, S, T, M, or V; A1247 replaced with G, I, L, S, T, M, or V; V1248 replaced with A, G, I, L, S, T, or M; T1249 replaced with A, G, I, L, S, M, or V; L1250 replaced with A, G, I, S, T, M, or V; A1251 replaced with G, I, L, S, T, M, or V; G1252 replaced with A, I, L, S, T, M, or V; K1253 replaced with H, or R; L1255 replaced with A, G, I, S, T, M, or V; V1256 replaced with A, G, I, L, S, T, or M; K1257 replaced with H, or R; T1258 replaced with A, G, I, L, S, M, or V; S1259 replaced with A, G, I, L, T, M, or V; R1260 replaced with H, or K; M1261 replaced with A, G, I, L, S, T, or V; T1262 replaced with A, G, I, L, S, M, or V; V1263 replaced with A, G, I, L, S, T, or M; I1264 replaced with A, G, L, S, T, M, or V; N1265 replaced with Q; T1266 replaced with A, G, I, L, S, M, or V; E1267 replaced with D; K1268 replaced with H, or R; A1270 replaced with G, I, L, S, T, M, or V; V1271 replaced with A, G, I, L, S, T, or M; T1272 replaced with A, G, I, L, S, M, or V; V1273 replaced with A, G, I, L, S, T, or M; D1274 replaced with E; I1275 replaced with A, G, L, S, T, M, or V; G1276 replaced with A, I, L, S, T, M, or V; S1277 replaced with A, G, I, L, T, M, or V; T1278 replaced with A, G, I, L, S, M, or V; I1279 replaced with A, G, L, S, T, M, or V; K1280 replaced with H, or R; T1281 replaced with A, G, I, L, S, M, or V; V1282 replaced with A, G, I, L, S, T, or M; Q1283 replaced with N; G1284 replaced with A, I, L, S, T, M, or V; V1285 replaced with A, G, I, L, S, T, or M; N1286 replaced with Q; V1287 replaced with A, G, I, L, S, T, or M; T1288 replaced with A, G, I, L, S, M, or V; I1289 replaced with A, G, L, S, T, M, or V; N1290 replaced with Q; Q1292 replaced with N; V1293 replaced with A, G, I, L, S, T, or M; A1294 replaced with G, I, L, S, T, M, or V; G1295 replaced with A, I, L, S, T, M, or V; V1296 replaced with A, G, I, L, S, T, or M; E1298 replaced with D; A1299 replaced with G, I, L, S, T, M; or V; E1300 replaced with D; V1301 replaced with A, G, I, L, S, T, or M; T1302 replaced with A, G, I, L, S, M, or V; W1303 replaced with F, or Y; F1304 replaced with W, or Y; R1305 replaced with H, or K; N1306 replaced with Q; K1307 replaced with H, or R; S1308 replaced with A, G, I, L, T, M, or V; K1309 replaced with H, or R; L1310 replaced with A, G, I, S, T, M, or V; G1311 replaced with A, I, L, S, T, M, or V; S1312 replaced with A, G, I, L, T, M, or V; H1314 replaced with K, or R; H1315 replaced with K, or R; L1316 replaced with A, G, I, S, T, M, or V; H1317 replaced with K, or R; E1318 replaced with D; G1319 replaced with A, I, L, S, T, M, or V; S1320 replaced with A, G, I, L, T, M, or V; L1321 replaced with A, G, I, S, T, M, or V; L1322 replaced with A, G, I, S, T, M, or V; L1323 replaced with A, G, I, S, T, M, or V; T1324 replaced with A, G, I, L, S, M, or V; N1325 replaced with Q; V1326 replaced with A, G, I, L, S, T, or M; S1327 replaced with A, G, I, L, T, M, or V; S1328 replaced with A, G, I, L, T, M, or V; S1329 replaced with A, G, I, L, T, M, or V; D1330 replaced with E; Q1331 replaced with N; G1332 replaced with A, I, L, S, T, M, or V; L1333 replaced with A, G, I, S, T, M, or V; Y1334 replaced with F, or W; S1335 replaced with A, G, I, L, T, M, or V; R1337 replaced with H, or K; A1338 replaced with G, I, L, S, T, M, or V; A1339 replaced with G, I, L, S, T, M, or V; N1340 replaced with Q; L1341 replaced with A, G, I, S, T, M, or V; H1342 replaced with K, or R; G1343 replaced with A, I, L, S, T, M, or V; E1344 replaced with D; L1345 replaced with A, G, I, S, T, M, or V; T1346 replaced with A, G, I, L, S, M, or V; E1347 replaced with D; S1348 replaced with A, G, I, L, T, M, or V; T1349 replaced with A, G, I, L, S, M, or V; Q1350 replaced with N; L1351 replaced with A, G, I, S, T, M, or V; L1352 replaced with A, G, I, S, T, M, or V; I1353 replaced with A, G, L, S, T, M, or V; L1354 replaced with A, G, I, S, T, M, or V; D1355 replaced with E; Q1358 replaced with N; V1359 replaced with A, G, I, L, S, T, or M; T1361 replaced with A, G, I, L, S, M, or V; Q1362 replaced with N; L1363 replaced with A, G, I, S, T, M, or V; E1364 replaced with D; D1365 replaced with E; I1366 replaced with A, G, L, S, T, M, or V; R1367 replaced with H, or K; A1368 replaced with G, I, L, S, T, M, or V; L1369 replaced with A, G, I, S, T, M, or V; L1370 replaced with A, G, I, S, T, M, or V; A1371 replaced with G, I, L, S, T, M, or V; A1372 replaced with G, I, L, S, T, M, or V; T1373 replaced with A, G, I, L, S, M, or V; G1374 replaced with A, I, L, S, T, M, or V; N1376 replaced with Q; L1377 replaced with A, G, I, S, T, M, or V; S1379 replaced with A, G, I, L, T, M, or V; V1380 replaced with A, G, I, L, S, T, or M; L1381 replaced with A, G, I, S, T, M, or V; T1382 replaced with A, G, I, L, S, M, or V; S1383 replaced with A, G, I, L, T, M, or V; L1385 replaced with A, G, I, S, T, M, or V; G1386 replaced with A, I, L, S, T, M, or V; T1387 replaced with A, G, I, L, S, M, or V; Q1388 replaced with N; L1389 replaced with A, G, I, S, T, M, or V; V1390 replaced with A, G, I, L, S, T, or M; L1391 replaced with A, G, I, S, T, M, or V; D1392 replaced with E; G1394 replaced with A, I, L, S, T, M, or V; N1395 replaced with Q; S1396 replaced with A, G, I, L, T, M, or V; A1397 replaced with G, I, L, S, T, M, or V; L1398 replaced with A, G, I, S, T, M, or V; L1399 replaced with A, G, I, S, T, M, or V; G1400 replaced with A, I, L, S, T, M, or V; I1403 replaced with A, G, L, S, T, M, or V; K1404 replaced with H, or R; G1405 replaced with A, I, L, S, T, M, or V; H1406 replaced with K, or R; V1408 replaced with A, G, I, L, S, T, or M; N1410 replaced with Q; I1411 replaced with A, G, L, S, T, M, or V; T1412 replaced with A, G, I, L, S, M, or V; W 1413 replaced with F, or Y; F1414 replaced with W, or Y; H1415 replaced with K, or R; G1416 replaced with A, I, L, S, T, M, or V; G1417 replaced with A, I, L, S, T, M, or V; Q1418 replaced with N; I1420 replaced with A, G, L, S, T, M, or V; V1421 replaced with A, G, I, L, S, T, or M; T1422 replaced with A, G, I, L, S, M, or V; A1423 replaced with G, I, L, S, T, M, or V; T1424 replaced with A, G, I, L, S, M, or V; G1425 replaced with A, I, L, S, T, M, or V; L1426 replaced with A, G, I, S, T, M, or V; T1427 replaced with A, G, I, L, S, M, or V; H1428 replaced with K, or R; H1429 replaced with K, or R; I1430 replaced with A, G, L, S, T, M, or V; L1431 replaced with A, G, I, S, T, M, or V; A1432 replaced with G, I, L, S, T, M, or V; A1433 replaced with G, I, L, S, T, M, or V; G1434 replaced with A, I, L, S, T, M, or V; Q1435 replaced with N; I1436 replaced with A, G, L, S, T, M, or V; L1437 replaced with A, G, I, S, T, M, or V; Q1438 replaced with N; V1439 replaced with A, G, I, L, S, T, or M; A1440 replaced with G, I, L, S, T, M, or V; N1441 replaced with Q; L1442 replaced with A, G, I, S, T, M, or V; S1443 replaced with A, G, I, L, T, M, or V; G1444 replaced with A, I, L, S, T, M, or V; G1445 replaced with A, I, L, S, T, M, or V; S1446 replaced with A, G, I, L, T, M, or V; Q1447 replaced with N; G1448 replaced with A, I, L, S, T, M, or V; E1449 replaced with D; F1450 replaced with W, or Y; S1451 replaced with A, G, I, L, T, M, or V; L1453 replaced with A, G, I, S, T, M, or V; A1454 replaced with G, I, L, S, T, M, or V; Q1455 replaced with N; N1456 replaced with Q; E1457 replaced with D; A1458 replaced with G, I, L, S, T, M, or V; G1459 replaced with A, I, L, S, T, M, or V; V1460 replaced with A, G, I, L, S, T, or M; L1461 replaced with A, G, I, S, T, M, or V; M1462 replaced with A, G, I, L, S, T, or V; Q1463 replaced with N; K1464 replaced with H, or R; A1465 replaced with G, I, L, S, T, M, or V; S1466 replaced with A, G, I, L, T, M, or V; L1467 replaced with A, G, I, S, T, M, or V; V1468 replaced with A, G, I, L, S, T, or M; I1469 replaced with A, G, L, S, T, M, or V; Q1470 replaced with N; D1471 replaced with E; Y1472 replaced with F, or W; W1473 replaced with F, or Y; W1474 replaced with F, or Y; S1475 replaced with A, G, I, L, T, M, or V; V1476 replaced with A, G, I, L, S, T, or M; D1477 replaced with E; R1478 replaced with H, or K; L1479 replaced with A, G, I, S, T, M, or V; A1480 replaced with G, I, L, S, T, M, or V; T1481 replaced with A, G, I, L, S, M, or V; S1483 replaced with A, G, I, L, T, M, or V; A1484 replaced with G, I, L, S, T, M, or V; S1485 replaced with A, G, I, L, T, M, or V; G1487 replaced with A, I, L, S, T, M, or V; N1488 replaced with Q; R1489 replaced with H, or K; G1490 replaced with A, I, L, S, T, M, or V; V1491 replaced with A, G, I, L, S, T, or M; Q1492 replaced with N; Q1493 replaced with N; R1495 replaced with H, or K; L1496 replaced with A, G, I, S, T, M, or V; R1497 replaced with H, or K; L1499 replaced with A, G, I, S, T, M, or V; L1500 replaced with A, G, I, S, T, M, or V; N1501 replaced with Q; S1502 replaced with A, G, I, L, T, M, or V; T1503 replaced with A, G, I, L, S, M, or V; E1504 replaced with D; V1505 replaced with A, G, I, L, S, T, or M; N1506 replaced with Q; A1508 replaced with G, I, L, S, T, M, or V; H1509 replaced with K, or R; A1511 replaced with G, I, L, S, T, M, or V; G1512 replaced with A, I, L, S, T, M, or V; K1513 replaced with H, or R; V1514 replaced with A, G, I, L, S, T, or M; R1515 replaced with H, or K; A1517 replaced with G, I, L, S, T, M, or V; V1518 replaced with A, G, I, L, S, T, or M; Q1519 replaced with N; I1521 replaced with A, G, L, S, T, M, or V; A1522 replaced with G, I, L, S, T, M, or V; N1524 replaced with Q; R1525 replaced with H, or K; R1526 replaced with H, or K; D1527 replaced with E; S1530 replaced with A, G, I, L, T, M, or V; R1531 replaced with H, or K; W1532 replaced with F, or Y; M1533 replaced with A, G, I, L, S, T, or V; V1534 replaced with A, G, I, L, S, T, or M; T1535 replaced with A, G, I, L, S, M, or V; S1536 replaced with A, G, I, L, T, M, or V; W1537 replaced with F, or Y; S1538 replaced with A, G, I, L, T, M, or V; A1539 replaced with G, I, L, S, T, M, or V; T1541 replaced with A, G, I, L, S, M, or V; R1542 replaced with H, or K; S1543 replaced with A, G, I, L, T, M, or V; G1545 replaced with A, I, L, S, T, M, or V; G1546 replaced with A, I, L, S, T, M, or V; G1547 replaced with A, I, L, S, T, M, or V; V1548 replaced with A, G, I, L, S, T, or M; Q1549 replaced with N; T1550 replaced with A, G, I, L, S, M, or V; R1551 replaced with H, or K; R1552 replaced with H, or K; V1553 replaced with A, G, I, L, S, T, or M; T1554 replaced with A, G, I, L, S, M, or V; Q1556 replaced with N; K1557 replaced with H, or R; L1558 replaced with A, G, I, S, T, M, or V; K1559 replaced with H, or R; A1560 replaced with G, I, L, S, T, M, or V; S1561 replaced with A, G, I, L, T, M, or V; G1562 replaced with A, I, L, S, T, M, or V; I1563 replaced with A, G, L, S, T, M, or V; S1564 replaced with A, G, I, L, T, M, or V; T1565 replaced with A, G, I, L, S, M, or V; V1567 replaced with A, G, I, L, S, T, or M; S1568 replaced with A, G, I, L, T, M, or V; N1569 replaced with Q; D1570 replaced with E; M1571 replaced with A, G, I, L, S, T, or V; T1573 replaced with A, G, I, L, S, M, or V; Q1574 replaced with N; V1575 replaced with A, G, I, L, S, T, or M; A1576 replaced with G, I, L, S, T, M, or V; K1577 replaced with H, or R; R1578 replaced with H, or K; V1580 replaced with A, G, I, L, S, T, or M; D1581 replaced with E; T1582 replaced with A, G, I, L, S, M, or V; Q1583 replaced with N; A1584 replaced with G, I, L, S, T, M, or V; N1586 replaced with Q; Q1587 replaced with N; Q1588 replaced with N; L1589 replaced with A, G, I, S, T, M, or V; V1591 replaced with A, G, I, L, S, T, or M; E1592 replaced with D; W1593 replaced with F, or Y; A1594 replaced with G, I, L, S, T, M, or V; F1595 replaced with W, or Y; S1596 replaced with A, G, I, L, T, M, or V; S1597 replaced with A, G, I, L, T, M, or V; W1598 replaced with F, or Y; G1599 replaced with A, I, L, S, T, M, or V; Q1600 replaced with N; N1602 replaced with Q; G1603 replaced with A, I, L, S, T, M, or V; I1606 replaced with A, G, L, S, T, M, or V; G1607 replaced with A, I, L, S, T, M, or V; H1609 replaced with K, or R; L1610 replaced with A, G, I, S, T, M, or V; A1611 replaced with G, I, L, S, T, M, or V; V1612 replaced with A, G, I, L, S, T, or M; Q1613 replaced with N; H1614 replaced with K, or R; R1615 replaced with H, or K; Q1616 replaced with N; V1617 replaced with A, G, I, L, S, T, or M; F1618 replaced with W, or Y; Q1620 replaced with N; T1621 replaced with A, G, I, L, S, M, or V; R1622 replaced with H, or K; D1623 replaced with E; G1624 replaced with A, I, L, S, T, M, or V; I1625 replaced with A, G, L, S, T, M, or V; T1626 replaced with A, G, I, L, S, M, or V; L1627 replaced with A, G, I, S, T, M, or V; S1629 replaced with A, G, I, L, T, M, or V; E1630 replaced with D; Q1631 replaced with N; S1633 replaced with A, G, I, L, T, M, or V; A1634 replaced with G, I, L, S, T, M, or V; L1635 replaced with A, G, I, S, T, M, or V; R1637 replaced with H, or K; V1639 replaced with A, G, I, L, S, T, or M; S1640 replaced with A, G, I, L, T, M, or V; T1641 replaced with A, G, I, L, S, M, or V; Q1642 replaced with N; N1643 replaced with Q; W1645 replaced with F, or Y; S1646 replaced with A, G, I, L, T, M, or V; E1647 replaced with D; A1648 replaced with G, I, L, S, T, M, or V; S1650 replaced with A, G, I, L, T, M, or V; V1651 replaced with A, G, I, L, S, T, or M; H1652 replaced with K, or R; W1653 replaced with F, or Y; R1654 replaced with H, or K; V1655 replaced with A, G, I, L, S, T, or M; S1656 replaced with A, G, I, L, T, M, or V; L1657 replaced with A, G, I, S, T, M, or V; W1658 replaced with F, or Y; T1659 replaced with A, G, I, L, S, M, or V; L1660 replaced with A, G, I, S, T, M, or V; T1662 replaced with A, G, I, L, S, M, or V; A1663 replaced with G, I, L, S, T, M, or V; T1664 replaced with A, G, I, L, S, M, or V; G1666 replaced with A, I, L, S, T, M, or V; N1667 replaced with Q; Y1668 replaced with F, or W; G1669 replaced with A, I, L, S, T, M, or V; F1670 replaced with W, or Y; Q1671 replaced with N; S1672 replaced with A, G, I, L, T, M, or V; R1673 replaced with H, or K; R1674 replaced with H, or K; V1675 replaced with A, G, I, L, S, T, or M; E1676 replaced with D; V1678 replaced with A, G, I, L, S, T, or M; H1679 replaced with K, or R; A1680 replaced with G, I, L, S, T, M, or V; R1681 replaced with H, or K; T1682 replaced with A, G, I, L, S, M, or V; N1683 replaced with Q; K1684 replaced with H, or R; A1685 replaced with G, I, L, S, T, M, or V; V1686 replaced with A, G, I, L, S, T, or M; E1688 replaced with D; H1689 replaced with K, or R; L1690 replaced with A, G, I, S, T, M, or V; S1692 replaced with A, G, I, L, T, M, or V; W1693 replaced with F, or Y; G1694 replaced with A, I, L, S, T, M, or V; R1696 replaced with H, or K; A1698 replaced with G, I, L, S, T, M, or V; N1699 replaced with Q; W1700 replaced with F, or Y; Q1701 replaced with N; R1702 replaced with H, or K; N1704 replaced with Q; I1705 replaced with A, G, L, S, T, M, or V; T1706 replaced with A, G, I, L, S, M, or V; E1709 replaced with D; N1710 replaced with Q; M1711 replaced with A, G, I, L, S, T, or V; E1712 replaced with D; R1714 replaced with H, or K; D1715 replaced with E; T1716 replaced with A, G, I, L, S, M, or V; T1717 replaced with A, G, I, L, S, M, or V; R1718 replaced with H, or K; Y1719 replaced with F, or W; E1721 replaced with D; K1722 replaced with H, or R; V1723 replaced with A, G, I, L, S, T, or M; K1724 replaced with H, or R; Q1725 replaced with N; L1726 replaced with A, G, I, S, T, M, or V; K1727 replaced with H, or R; L1728 replaced with A, G, I, S, T, M, or V; Q1730 replaced with N; L1731 replaced with A, G, I, S, T, M, or V; S1732 replaced with A, G, I, L, T, M, or V; Q1733 replaced with N; F1734 replaced with W, or Y; K1735 replaced with H, or R; S1736 replaced with A, G, I, L, T, M, or V; R1737 replaced with H, or K; G1740 replaced with A, I, L, S, T, M, or V; T1741 replaced with A, G, I, L, S, M, or V; G1743 replaced with A, I, L, S, T, M, or V; K1744 replaced with H, or R; or A1745 replaced with G, I, L, S, T, M, or V.
The resulting constructs can be routinely screened for activities or functions described throughout the specification and known in the art. Preferably, the resulting constructs have an increased THRAP activity or function, while the remaining THRAP activities or functions are maintained. More preferably, the resulting constructs have more than one increased THRAP activity or function, while the remaining THRAP activities or functions are maintained.
Besides conservative amino acid substitution, non-conservative substitutions are also preferred. For example, preferred non-conservative substitutions of THRAP (SEQ ID NO:89) include: M1 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E2 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C3 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; C4 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R5 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R6 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A7 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T8 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P9 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G10 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T11 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L12 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L13 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L14 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F15 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L16 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A17 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F18 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L19 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L20 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L21 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S22 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S23 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R24 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T25 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A26 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R27 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S28 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E29 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E30 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D31 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R32 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D33 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G34 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L35 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W36 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D37 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A38 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W39 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G40 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P41 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; W42 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S43 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E44 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C45 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S46 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R47 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T48 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C49 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G50 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G51 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G52 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A53 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S54 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y55 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S56 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L57 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R58 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R59 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C60 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L61 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S62 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S63 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K64 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S65 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C66 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; E67 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G68 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R69 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N70 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I71 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R72 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y73 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R74 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T75 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C76 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S77 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N78 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V79 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D80 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C81 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P82 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P83 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E84 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A85 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G86 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D87 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F88 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R89 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A90 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q91 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q92 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C93 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S94 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A95 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H96 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N97 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D98 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V99 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K100 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H101 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H102 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G103 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q104 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; F105 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y106 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E107 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W108 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L109 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P110 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V111 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S112 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N 113 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D114 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P115 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; D116 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N 117 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P118 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C119 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S120 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L121 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K122 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C123 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q124 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A125 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K126 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G127 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T128 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T129 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L130 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V131 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V132 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E133 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L134 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A135 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P136 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K137 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V138 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L139 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D140 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G141 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T142 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R143 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C144 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Y145 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T146 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E147 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S148 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L149 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D150 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M151 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C152 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; I153 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S154 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G155 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L156 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C157 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q158 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I159 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V160 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G161 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C162 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; D163 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H164 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q165 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L166 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G167 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S168 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T169 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V170 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K171 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E172 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D173 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N174 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C175 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G176 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V177 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C178 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N179 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G180 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D181 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G182 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S183 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T184 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C185 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R186 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L187 replaced with, E, H, K, R, N, Q, F, W, Y, P, or C; V188 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R189 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G190 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q191 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Y192 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K193 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S194 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q195 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L196 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S197 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A198 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T199 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K200 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S201 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D202 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D203 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T204 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V205 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V206 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A207 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I208 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P209 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; Y210 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G211 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S212 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R213 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H214 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I215 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R216 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L217 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V218 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L219 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K220 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G221 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P222 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; D223 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H224 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L225 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y226 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L227 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E228 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T229 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K230 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T231 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L232 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q233 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G234 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T235 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K236 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G237 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E238 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N239 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S240 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L241 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S242 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S243 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T244 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G245 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T246 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F247 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L248 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V249 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D250 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N251 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S252 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S253 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V254 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D255 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F256 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q257 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K258 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F259 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; P260 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; D261 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K262 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E263 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I264 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L265 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R266 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M267 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A268 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G269 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P270 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L271 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T272 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A273 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D274 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F275 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I276 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V277 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K278 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I279 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R280 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N281 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S282 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G283 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S284 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A285 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D286 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S287 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T288 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V289 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q290 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; F291 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I292 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F293 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y294 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q295 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P296 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I297 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I298 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H299 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R300 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W301 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R302 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E303 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T304 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D305 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F306 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F307 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; P308 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C309 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S310 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A311 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T312 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C313 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G314 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G315 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G316 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y317 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q318 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L319 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T320 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S321 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A322 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E323 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C324 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Y325 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D326 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L327 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R328 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S329 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N330 replaced with D, E, H, K, R, A, G, J, L, S, T, M, V, F, W, Y, P, or C; R331 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V332 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V333 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A334 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D335 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q336 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Y337 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; C338 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; H339 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y340 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y341 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; P342 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E343 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N344 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I345 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K346 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P347 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K348 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P349 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K350 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L351 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q352 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E353 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C354 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N355 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L356 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D357 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P358 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C359 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P360 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A361 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R362 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W363 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E364 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A365 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T366 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P367 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; W368 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T369 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A370 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C371 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S372 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S373 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S374 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C375 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G376 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G377 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G378 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I379 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q380 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S381 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R382 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A383 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V384 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S385 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C386 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; V387 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E388 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E389 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D390 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I391 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q392 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G393 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H394 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V395 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T396 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S397 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V398 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E399 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E400 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W401 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K402 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C403 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; M404 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y405 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T406 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P407 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K408 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M409 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P410 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I411 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A412 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q413 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P414 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C415 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N416 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I417 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F418 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D419 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C420 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P421 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K422 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W423 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L424 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A425 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q426 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E427 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W428 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S429 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P430 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C431 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; T432 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V433 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T434 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C435 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G436 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q437 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G438 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L439 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R440 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y441 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R442 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V443 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V444 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L445 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C446 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; I447 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D448 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H449 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R450 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G451 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M452 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H453 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T454 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G455 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G456 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C457 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S458 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P459 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K460 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T461 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K462 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P463 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H464 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I465 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K466 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E467 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E468 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C469 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; I470 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V471 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P472 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; T473 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P474 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C475 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Y476 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K477 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P478 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K479 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E480 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K481 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L482 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P483 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V484 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E485 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A486 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K487 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L488 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P489 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; W490 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F491 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K492 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q493 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A494 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q495 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E496 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L497 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E498 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E499 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G500 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A501 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A502 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V503 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S504 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E505 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E506 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P507 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S508 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F509 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I510 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P511 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K512 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A513 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W514 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S515 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A516 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C517 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; T518 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V519 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T520 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C521 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G522 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V523 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G524 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T525 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q526 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V527 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R528 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I529 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V530 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R531 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C532 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q533 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V534 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L535 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L536 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S537 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F538 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S539 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q540 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S541 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V542 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A543 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D544 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L545 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P546 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I547 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D548 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E549 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C550 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; E551 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G552 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P553 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K554 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P555 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A556 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S557 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q558 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R559 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A560 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C561 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Y562 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A563 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G564 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P565 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C566 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S567 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G568 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E569 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I570 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P571 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E572 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F573 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; N574 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P575 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; D576 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E577 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T578 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D579 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G580 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L581 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F582 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G583 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G584 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L585 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q586 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D587 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F588 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D589 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E590 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L591 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y592 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D593 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W594 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E595 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y596 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E597 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G598 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F599 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T600 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K601 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C602 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S603 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E604 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S605 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C606 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G607 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G608 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G609 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V610 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q611 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E612 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A613 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V614 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V615 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S616 replaced with D E, H, K, R, N, Q, F, W, Y, P, or C; C617 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L618 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N619 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K620 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q621 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T622 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R623 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E624 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P625 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A626 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E627 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E628 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N629 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L630 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C631 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; V632 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T633 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S634 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R635 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R636 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P637 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P638 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; Q639 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L640 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L641 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K642 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S643 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C644 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N645 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L646 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D647 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P648 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C649 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P650 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A651 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R652 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W653 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E654 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I655 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G656 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K657 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W658 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S659 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P660 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C661 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S662 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L663 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T664 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C665 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G666 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V667 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G668 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L669 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q670 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T671 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R672 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D673 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V674 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F675 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; C676 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S677 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H678 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L679 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L680 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S681 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R682 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E683 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M684 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N685 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E686 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T687 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V688 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; 1689 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L690 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A691 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D692 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E693 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L694 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C695 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R696 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q697 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P698 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K699 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P700 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S701 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T702 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V703 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q704 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A705 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C706 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N707 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R708 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F709 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; N710 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C711 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P712 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P713 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A714 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W715 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y716 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; P717 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A718 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q719 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; W720 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q721 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P722 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C723 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S724 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R725 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T726 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C727 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G728 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G729 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G730 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V731 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q732 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K733 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R734 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E735 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V736 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L737 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C738 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; K739 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q740 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R741 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M742 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A743 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D744 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G745 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S746 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F747 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L748 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E749 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L750 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P751 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E752 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T753 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F754 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; C755 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S756 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A757 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S758 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K759 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P760 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A761 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C762 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q763 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q764 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A765 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C766 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; K767 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K768 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D769 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D770 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C771 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P772 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S773 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E774 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W775 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L776 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L777 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S778 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D779 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W780 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T781 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E782 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C783 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S784 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T785 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S786 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C787 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G788 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E789 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G790 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T791 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q792 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T793 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R794 replaced with D, E, A, G, J, L, S, T, M, V, N, Q, F, W, Y, P, or C; S795 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A796 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I797 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C798 replaced with D, E, H, K, R, A, G, J, L, S, T, M, V, N, Q, F, W, Y, or P; R799 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K800 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M801 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L802 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K803 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T804 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G805 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L806 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S807 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T808 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V809 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V810 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N811 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S812 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T813 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L814 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C815 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P816 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P817 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L818 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P819 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; F820 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S821 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S822 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S823 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I824 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R825 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P826 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C827 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; M828 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L829 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A830 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T831 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C832 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; A833 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R834 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P835 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G836 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R837 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P838 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S839 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T840 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K841 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H842 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S843 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P844 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H845 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I846 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A847 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A848 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A849 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R850 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K851 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V852 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y853 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; I854 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q855 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T856 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R857 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R858 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q859 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R860 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K861 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L862 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H863 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F864 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; V865 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V866 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G867 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G868 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F869 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A870 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y871 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L872 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L873 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P874 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K875 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T876 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A877 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V878 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V879 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L880 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R881 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C882 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P883 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A884 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R885 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R886 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V887 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R888 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K889 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P890 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L891 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I892 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T893 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W894 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E895 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K896 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D897 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G898 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q899 replaced with D, E, H, K, R, A, C, I, L, S, T, M, V, F, W, Y, P, or C; H900 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L901 replaced with D, B, H, K, R, N, Q, F, W, Y, P, or C; I902 replaced with D, B, H, K, R, N, Q, F, W, Y, P, or C; S903 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S904 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T905 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H906 replaced with D, E, A, C, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V 907 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T 908 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V909 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A910 replaced with D, B, H, K, R, N, Q, F, W, Y, P, or C; P911 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; F912 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G913 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y914 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; L915 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K916 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I917 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H918 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R919 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L920 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K921 replaced with D, E, A, C, G, L, S, T, M, V, N, Q, F, W, Y, P, or C; P922 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S923 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D924 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A925 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G926 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V927 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y928 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T929 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C930 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S931 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A932 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G933 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P934 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A935 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R936 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E937 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H938 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F939 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; V940 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I941 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K942 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L943 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I944 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G945 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G946 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N947 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R948 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K949 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L950 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V951 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A952 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R953 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P954 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L955 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S956 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P957 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R958 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S959 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E960 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E961 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E962 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V963 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L964 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A965 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G966 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R967 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K968 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G969 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G970 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P971 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; K972 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E973 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A974 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L975 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q976 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T977 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H978 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K979 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H980 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q981 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; N982 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G983 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I984 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F985 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S986 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N987 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G988 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S989 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K990 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A991 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E992 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K993 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R994 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G995 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L996 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A997 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A998 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N999 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1000 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G1001 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1002 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1003 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y1004 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D1005 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1006 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1007 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1008 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1009 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1010 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1011 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1012 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1013 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1014 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1015 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1016 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1017 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; P1018 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G1019 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1020 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1021 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1022 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1023 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1024 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1025 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; E1026 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1027 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1028 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D1029 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1030 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1031 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1032 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1033 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N1034 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T1035 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1036 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1037 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1038 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E1039 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1040 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1041 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G1042 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1043 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1044 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1045 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1046 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1047 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1048 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1049 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1050 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1051 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; F1052 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T1053 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M1054 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1055 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1056 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1057 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1058 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R1059 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1060 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1061 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1062 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1063 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1064 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1065 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1066 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1067 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1068 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1069 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1070 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q1071 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1072 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E1073 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E1074 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1075 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1076 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1077 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1078 replaced with D, E, H, K, R, N, Q, F. W, Y, P, or C; Y1079 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1080 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1081 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1082 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1083 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1084 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1085 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1086 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1087 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1088 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1089 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E1090 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1091 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F1092 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R1093 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1094 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1095 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1096 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1097 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1098 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1099 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D1100 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1101 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1102 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1103 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1104 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1105 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S1106 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1107 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1108 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1109 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1110 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1111 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1112 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1113 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1114 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1115 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1116 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1117 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H1118 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K1119 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1120 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1121 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1122 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1123 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F 1124 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1125 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1126 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1127 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1128 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1129 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1130 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1131 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1132 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1133 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1134 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1135 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1136 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1137 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1138 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G 1139 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1140 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1141 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1142 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1143 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H1144 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1145 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K1146 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1147 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; T1148 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1149 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1150 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1151 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K1152 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1153 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1154 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1155 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1156 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1157 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q1158 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1159 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1160 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1161 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1162 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1163 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1164 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V 1165 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1166 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1167 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1168 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1169 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1170 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T1171 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1172 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1173 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1174 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1175 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1176 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1177 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1178 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1179 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1180 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1181 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1182 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1183 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1184 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1185 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; E1186 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1187 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1188 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1189 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1190 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1191 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R1192 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1193 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; T1194 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1195 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1196 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1197 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A1198 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1199 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N1200 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1201 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1202 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E1203 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1204 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1205 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; F1206 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1207 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1208 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1209 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1210 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1211 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1212 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1213 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1214 replaced with D, E, H, K, R, A, G, J, L, S, T, M, V, N, Q, F, W, Y, or C; D1215 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1216 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1217 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1218 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1219 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I1220 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1221 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1222 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1223 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1224 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1225 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1226 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1227 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1228 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1229 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F1230 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Y1231 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T1232 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1233 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N1234 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A1235 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1236 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1237 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A1238 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1239 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1240 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y1241 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; D1242 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1243 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1244 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1245 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1246 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1247 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1248 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1249 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1250 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1251 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1252 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1253 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1254 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L1255 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1256 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1257 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1258 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1259 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1260 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M1261 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1262 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1263 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1264 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1265 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T1266 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1267 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K1268 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1269 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A1270 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1271 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1272 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1273 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1274 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1275 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1276 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1277 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1278 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1279 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1280 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1281 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1282 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1283 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1284 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1285 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1286 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1287 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1288 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1289 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1290 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C1291 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q1292 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1293 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1294 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1295 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1296 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1297 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E1298 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1299 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1300 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1301 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1302 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1303 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F1304 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R1305 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N1306 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K1307 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1308 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1309 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1310 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1311 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1312 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1313 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H1314 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1315 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1316 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1317 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; E1318 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1319 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1320 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1321 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1322 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1323 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1324 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1325 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1326 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1327 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1328 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1329 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1330 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1331 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1332 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1333 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Y1334 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1335 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1336 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R1337 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1338 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1339 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1340 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1341 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1342 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1343 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1344 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1345 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1346 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1347 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1348 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1349 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1350 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1351 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1352 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1353 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1354 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1355 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1356 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; P1357 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; Q1358 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1359 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1360 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; T1361 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1362 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1363 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1364 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1365 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1366 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1367 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1368 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1369 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1370 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1371 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1372 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1373 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1374 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1375 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; N1376 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1377 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1378 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S1379 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1380 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1381 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1382 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1383 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1384 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; L1385 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1386 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1387 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1388 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1389 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1390 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1391 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1392 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1393 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; G1394 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1395 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S1396 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1397 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1398 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1399 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1400 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1401 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P1402 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I1403 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1404 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1405 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1406 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1407 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1408 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1409 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; N1410 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I1141 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1412 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1413 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; F1414 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; H1415 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1416 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1417 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1418 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1419 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I1420 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1421 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1422 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1423 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1424 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1425 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1426 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1427 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1428 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1429 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; I1430 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1431 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1432 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1433 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1434 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1435 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I1436 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1437 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1438 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1439 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1440 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1441 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1442 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1443 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1444 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1445 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1446 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1447 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1448 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1449 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; F1450 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1451 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1452 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L1453 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1454 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1455 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; N1456 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; E1457 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1458 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1459 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1460 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1461 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; M1462 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1463 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K1464 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1465 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1466 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1467 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1468 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1469 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1470 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D1471 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y1472 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; W1473 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; W1474 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1475 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1476 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1477 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1478 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1479 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1480 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1481 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1482 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S1483 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1484 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1485 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1486 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G1487 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1488 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R1489 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1490 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1491 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1492 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q1493 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1494 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R1495 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1496 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1497 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1498 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; L1499 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1500 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1501 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S1502 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1503 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1504 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1505 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1506 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1507 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A1508 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1509 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1510 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; A1511 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1512 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1513 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1514 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1515 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1516 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A1517 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1518 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1519 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; P1520 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; I1521 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1522 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1523 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N1524 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R1525 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1526 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1527 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1528 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; P1529 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S1530 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1531 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W1532 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; M1533 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1534 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1535 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1536 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1537 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1538 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1539 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1540 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; T1541 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1542 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1543 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1544 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G1545 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1546 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1547 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1548 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1549 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T1550 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1551 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1552 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1553 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1554 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1555 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q1556 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K1557 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1558 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1559 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1560 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1561 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1562 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1563 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1564 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1565 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1566 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1567 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1568 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1569 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; D1570 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; M1571 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1572 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; T1573 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1574 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1575 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1576 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1577 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1578 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1579 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1580 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; D1581 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1582 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1583 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; A1584 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1585 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N1586 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q1587 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Q1588 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1589 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1590 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; V1591 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1592 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W1593 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; A1594 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F1595 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1596 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1597 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1598 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G1599 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1600 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C1601 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N1602 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; G1603 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1604 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C1605 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; I1606 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; G1607 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1608 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; H1609 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1610 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1611 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1612 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1613 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; H1614 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1615 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1616 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; V1617 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F1618 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; C1619 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q1620 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; T1621 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1622 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1623 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; G1624 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; I1625 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1626 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1627 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1628 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; S1629 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1630 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1631 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C1632 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S1633 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1634 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1635 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1636 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R1637 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1638 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; V1639 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1640 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1641 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1642 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; N1643 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; C1644 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; W1645 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; S1646 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1647 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1648 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1649 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S1650 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1651 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1652 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; W1653 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; R1654 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1655 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1656 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1657 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1658 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; T1659 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; L1660 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1661 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; T1662 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; A1663 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1664 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1665 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G1666 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1667 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; Y1668 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G1669 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; F1670 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q1671 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; S1672 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1673 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; R1674 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1675 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1676 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1677 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; V1678 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; H1679 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1680 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1681 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1682 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1683 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; K1684 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; A1685 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; V1686 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1687 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; E1688 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; H1689 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1690 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1691 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; S1692 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; W1693 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; G1694 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1695 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; R1696 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; P1697 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; A1698 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; N1699 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; W1700 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; Q1701 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; R1702 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1703 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; N1704 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; I1705 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1706 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; P1707 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or C; C1708 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; E1709 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; N1710 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; M1711 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; E1712 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1713 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; R1714 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; D1715 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; T1716 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1717 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1718 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Y1719 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; C1720 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; E1721 replaced with H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; K1722 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; V1723 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1724 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; Q1725 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1726 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1727 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; L1728 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1729 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; Q1730 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; L1731 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; S1732 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; Q1733 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, F, W, Y, P, or C; F1734 replaced with D, E, H, K, R, N, Q, A, G, I, L, S, T, M, V, P, or C; K1735 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; S1736 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; R1737 replaced with D, E, A, G, I, L, S, T, M, V, N, Q, F, W, Y, P, or C; C1738 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; C1739 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G1740 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; T1741 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; C1742 replaced with D, E, H, K, R, A, G, I, L, S, T, M, V, N, Q, F, W, Y, or P; G1743 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C; K1744 replaced with D, E, A, G. I, L, S, T, M, V, N, Q, F, W, Y, P, or C; or A1745 replaced with D, E, H, K, R, N, Q, F, W, Y, P, or C. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
The resulting constructs can be routinely screened for activities or functions described throughout the specification and known in the art. Preferably, the resulting constructs have an decreased THRAP activity or function, while the remaining THRAP activities or functions are maintained. More preferably, the resulting constructs have more than one decreased THRAP activity or function, while the remaining THRAP activities or functions are maintained.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: prostate cancer, cancer of the gastrointestinal tract, disorders of the uterus, neurological disorders, synovial sarcoma, immune disorders, tumor growth, and/or cancer, in general. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune, neural, gastrointestinal, bone, skeletal, connective, and/or reproductive system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., immune, neural, gastrointestinal, bone, skeletal, connective, reproductive, cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, amniotic fluid, semen, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more of the immunogenic epitopes shown in SEQ ID NO: 89 as residues: Cys-3 to Pro-9, Arg-24 to Leu-35, Pro-41 to Gly-50, Lys-64 to Ser-77, Cys-93 to His-102, Ser-112 to Cys-119, Thr-142 to Ser-148, Val-170 to Gly-176, Arg-189 to Gln-195, Thr-235 to Leu-241, Arg-300 to Asp-305, Tyr-325 to Asn-330, Pro-342 to Asn-355, His-449 to Cys-457, Pro-459 to Lys-466, Pro-474 to Leu-482, Lys-492 to Leu-497, Glu-549 to Ser-557, Phe-573 to Gly-580, Tyr-596 to Cys-606, Asn-619 to Glu-627, Ser-634 to Leu-640, Trp-653 to Trp-658, Cys-695 to Ser-701, Pro-722 to Cys-727, Ala-765 to Ser-773, Thr-781 to Arg-794, Pro-835 to Pro-844, Thr-856 to Lys-861, Pro-883 to Arg-888, Leu-955 to Glu-960, Arg-967 to Ile-984, Asn-987 to Gly-995, Pro-1000 to Leu-1007, Gln-1028 to Gly-1042, Thr-1056 to Asp-1062, Leu-1068 to Tyr-1079, Pro-1105 to Ser-1111, Leu-1128 to Thr-1148, Arg-1305 to Gly-1311, Ser-1327 to Gly-1332, Cys-1486 to Arg-1495, Cys-1523 to Ser-1530, Gly-1666 to Arg-1674, Arg-1681 to Val-1686, Pro-1695 to Asn-1704, Pro-1707 to Arg-1718, Gln-1733 to Cys-1738. Polynucleotides encoding these polypeptides are also encompassed by the invention. Antibodies that bind one or more of these epitopes, domains described herein, or other polypeptides of the invention are specifically, but nonexclusively preferred.
The ubiquitous tissue distribution, the homology to thrombospondin-related protein, and the presence of multiple TSP-1-like domains indicates that the THRAP polypeptide and/or fragments of the present invention possess anti-angiogenic activity and, therefore, can be used in the treatment, diagnosis, and/or prevention of solid tumors of many tissues including, but not limited to the prostate, lung, breast, ovarian, stomach, pancreas, larynx, esophagus, testes, liver, parotid, biliary tract, colon, rectum, cervix, uterus, endometrium, kidney, bladder, thyroid cancer. Additionally, the THRAP polypeptide and/or fragments of the present invention can be used in the treatment, diagnosis, and/or prevention of primary tumors and metastases; melanomas; glioblastoma; Kaposi""s sarcoma; leiomyosarcoma; non-small cell lung cancer; colorectal cancer; advanced malignancies; and blood born tumors such as leukemias.
Additionally, the THRAP polypeptide and/or fragments of the present invention possess anti-angiogenic activity and, therefore, can be used in the treatment, diagnosis, and/or prevention of other disorders, besides cancers, which involve angiogenesis. These disorders include, but are not limited to: benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas; artheroscleric plaques; ocular angiogenic diseases, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, retrolental fibroplasia, rubeosis, restenosis, retinoblastoma, uvietis and Pterygia (abnormal blood vessel growth) of the eye; rheumatoid arthritis; psoriasis; delayed wound healing; endometriosis; vasculogenesis; granulations; hypertrophic scars (keloids); nonunion fractures; scleroderma; trachoma; vascular adhesions; myocardial angiogenesis; coronary collaterals; cerebral collaterals; arteriovenous malformations; ischemic limb angiogenesis; Osler-Webber Syndrome; plaque neovascularization; telangiectasia; hemophiliac joints; angiofibroma; fibromuscular dysplasia; wound granulation; Crohn""s disease; and/or atherosclerosis.
Moreover, the ubiquitous tissue distribution and the presence of proteinase inhibitor-like domains indicates that the THRAP polypeptide and/or fragments of the present invention are useful as a proteinase inhibitor.
The tissue distribution in brain and homology to thrombospondin-related protein indicates that the THRAP polypeptide and/or fragments of the present invention are useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it may play a role in normal neural function. Potentially, THRAP polypeptide and/or fragments of the present invention may be involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
The tissue distribution in immune cells and tissues (e.g., macrophage, and lymph node) and homology to thrombospondin-related protein indicates that the THRAP polypeptide and/or fragments of the present invention are useful for the detection, treatment, and/or prevention of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this THRAP polypeptide and/or fragments of the present invention indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. The expression within fetal tissue and other cellular sources marked by proliferating cells and homology to thrombospondin-related proteins indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation. Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA). Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus the THRAP polypeptide and/or fragments of the present invention may modulate apoptosis or tissue differentiation and would be useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The THRAP polypeptide and/or fragments of the present invention are useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The THRAP polypeptide and/or fragments of the present invention can also be used to gain new insight into the regulation of cellular growth and proliferation.
Additionally, the secreted protein can also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, and as nutritional supplements. It may also have a very wide range of biological activities. Representative uses are described in the xe2x80x9cChemotaxisxe2x80x9d and xe2x80x9cBinding Activityxe2x80x9d sections below, in Examples 11, 12, 13, 14, 15, 16, 18, 19, and 20, and elsewhere herein. Briefly, the THRAP polypeptide and/or fragments of the present invention may possess the following activities: cytokine, cell proliferation/differentiation modulating activity or induction of other cytokines; immunostimulating/immunosuppressant activities (e.g. for treating human immunodeficiency virus infection, cancer, autoimmune diseases and allergy); regulation of hematopoiesis (e.g. for treating anemia or as adjunct to chemotherapy); stimulation or growth of bone, cartilage, tendons, ligaments and/or nerves (e.g. for treating wounds, stimulation of follicle stimulating hormone (for control of fertility); chemotactic and chemokinetic activities (e.g. for treating infections, tumors); hemostatic or thrombolytic activity (e.g. for treating hemophilia, cardiac infarction etc.); anti-inflammatory activity (e.g. for treating septic shock, Crohn""s disease); as antimicrobials; for treating psoriasis or other hyperproliferative diseases; for regulation of metabolism, and behavior. Also contemplated is the use of the corresponding nucleic acid in gene therapy procedures. Polynucleotides of the invention may also be employed in gene therapy. Representative uses are of gene therapy are described in the section xe2x80x9cGene Therapyxe2x80x9d below and elsewhere herein.
Additionally, the expression of this gene product in synovium and homology to thrombospondin-related protein would suggest a role in the detection and treatment of disorders and conditions afflicting the skeletal system, in particular osteoporosis, bone cancer, connective tissue disorders (e.g. arthritis, trauma, tendonitis, chrondomalacia and inflammation). The THRAP polypeptide and/or fragments of the present invention are also useful in the diagnosis or treatment of various autoimmune disorders (i.e., rheumatoid arthritis, lupus, scleroderma, and dermatomyositis), dwarfism, spinal deformation, joint abnormalities, and chondrodysplasias (i.e. spondyloepiphyseal dysplasia congenita, familial osteoarthritis, Atelosteogenesis type II, metaphyseal chondrodysplasia type Schmid, etc.). Furthermore, the THRAP polypeptide and/or fragments of the present invention may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:18 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. However, preferably excluded from the present invention includes Genseq accession numbers Y35899, X97684, and X97583 (WO/9931236), which are hereby incorporated by reference in its entirety. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 5706 of SEQ ID NO:18, b is an integer of 15 to 5720, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:18, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 9
The translation product of this gene shares sequence homology with the mouse uterine-specific proline-rich acidic protein which may play an important role in pregnancy. Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with proline-rich acidic proteins. Such activities are known in the art, some of which are described elsewhere herein.
This gene is expressed primarily in colon cancer and to a lesser extent in fetal liver and spleen.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: colon cancer; digestive disorders; hematopoietic disorders; immune system dysfunction; inflammation; inflammatory bowel disease. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the colon and immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 90 as residues: Trp-35 to Trp-45, Pro-52 to Asp-57, Thr-73 to Thr-80, Pro-96 to Leu-103, Pro-106 to Arg-118, Pro-131 to Gln-142. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in colon cancer cells and tissues, combined with the homology to the mouse proline-rich acidic protein indicates that polynucleotides and polypeptides corresponding to this gene are useful for the diagnosis and/or treatment of disorders of the colon, including colon cancer. Elevated levels of this transcript in various colon tumors suggests that it may represent an important diagnostic or causative agent in the development or progression of colon cancer. Alternately, expression in the colon may be indicative of roles in normal colon or digestive function. Similarly, expression of this transcript in hematopoietic cells and tissues, such as fetal liver suggests that it may play a role in the proliferation, differentiation, survival, or activation of a variety of blood cell lineages. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:19 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 691 of SEQ ID NO:19, b is an integer of 15 to 705, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:19, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 10
The translation product of this gene shares sequence homology with bovine vacuolar ATP synthase membrane sector associated protein (see, e.g., Genbank Accession No. sp|P811341|VATN_BOVIN; all references available through this accession are hereby incorporated by reference in their entirety herein). Vacuolar ATPase is composed of at least 10 subunits and is believed to be responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
The polypeptide encoded by this gene has been determined to have a transmembrane domain at about amino acid position 307 to about 323 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing about amino acids 324 to about 350 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ia membrane proteins.
It has been discovered that this gene is expressed primarily in dendritic cells, human osteoclastoma, placenta, fetal liver spleen, infant brain, colon tumor, pancreatic tumor, and ovarian tumor.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: immune, skeletal, developmental, reproductive, and/or neural diseases or disorders. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune, hematopoietic, and/or integumentary system(s), expression of this gene at significantly higher or lower levels may be detected in certain tissues or cell types (e.g., immune, skeletal, developmental, reproductive, neural, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 91 as residues: Gln-153 to Ser-163, Ser-172 to Glu-178, Ala-204 to Asp-210, Ile-222 to Ala-236, Lys-284 to Ser-291, Met-342 to Arg-348. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in immune cells and tissues indicates that polynucleotides and/or polypeptides corresponding to this gene would be useful for the treatment, prevention, detection and/or diagnosis of hematopoietic related disorders such as anemia, pancytopenia, leukopenia, thrombocytopenia or leukemia since stromal cells are important in the production of cells of hematopoietic lineages. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the uses include bone marrow cell ex-vivo culture, bone marrow transplantation, bone marrow reconstitution, radiotherapy or chemotherapy of neoplasia. Polynucleotides and/or polypeptides of the invention may also be involved in lymphopoiesis, and therefore, would be useful in treating, preventing, detecting and/or diagnosing immune disorders such as infection, inflammation, allergy, immunodeficiency etc. In addition, this gene product may have commercial utility in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types.
Alternatively, polynucleotides and/or polypeptides corresponding to this gene would be useful in detecting, diagnosing, treating, and/or preventing congenital disorders (i.e., nevi, moles, freckles, Mongolian spots, hemangiomas, port-wine syndrome), integumentary tumors (i.e., keratoses, Bowen""s disease, basal cell carcinoma, squamous cell carcinoma, malignant melanoma, Paget""s disease, mycosis fungoides, and Kaposi""s sarcoma), injuries and inflammation of the skin (i.e., wounds, rashes, prickly heat disorder, psoriasis, dermatitis), atherosclerosis, uticaria, eczema, photosensitivity, autoimmune disorders (i.e., lupus erythematosus, vitiligo, dermatomyositis, morphea, scleroderma, pemphigoid, and pemphigus), keloids, striae, erythema, petechiae, purpura, and xanthelasma. In addition, such disorders may predispose increased susceptibility to viral and bacterial infections of the skin (i.e., cold sores, warts, chickenpox, molluscum contagiosum, herpes zoster, boils, cellulitis, erysipelas, impetigo, tinea, althlete""s foot, and ringworm). Moreover, the protein product of this clone may also be useful for the treatment or diagnosis of various connective tissue disorders (i.e., arthritis, trauma, tendonitis, chrondomalacia and inflammation, etc.), autoimmune disorders (i.e., rheumatoid arthritis, lupus, scleroderma, dermatomyositis, etc.), dwarfism, spinal deformation, joint abnormalities, and chondrodysplasias (i.e., spondyloepiphyseal dysplasia congenita, familial osteoarthritis, Atelosteogenesis type II, metaphyseal chondrodysplasia type Schmid). The predicted membrane localization indicates that polynucleotides and/or polypeptides corresponding to this gene would be a good target for antagonists, particularly small molecules or antibodies, which block functional activity (such as, for example, transport function; complex formation; binding of the receptor by its cognate ligand(s); signaling function). Accordingly, preferred are antibodies and or small molecules which specifically bind an extracellular portion of the translation product of this gene. The extracellular regions can be ascertained from the information regarding the transmembrane domains as set out above. Also provided is a kit for detecting tumors in which expression of this protein occurs (such as, for example, ovarian cancer). Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:20 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2094 of SEQ ID NO:20, b is an integer of 15 to 2108, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:20, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 11
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of, an amino acid sequence selected from the group consisting of:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in fetal heart, healing wounds, and keratinocytes.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: developmental, cardiovascular, and integumentary diseases and/or disorders, particularly vascular disorders and impaired wound healing. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the integumentary and immune systems, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., developmental, cardiovascular, integumentary, and cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 92 as residues: Ser-31 to Gly-45, Ser-54 to Gln-61, Ala-67 to Val-74. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in fetal heart indicates that polynucleotides and polypeptides corresponding to this gene are useful for the detection and/or treatment of vascular disorders including heart disease, myocardial infarction, ischemia, stroke, tumorigenesis, wound healing, ulcerative colitis, and skin disorders including psoriasis.
The tissue distribution in keratinocytes and healing wounds indicates that the protein product of this clone is useful for the treatment, diagnosis, and/or prevention of various skin disorders. Representative uses are described in the xe2x80x9cBiological Activityxe2x80x9d, xe2x80x9cHyperproliferative Disordersxe2x80x9d, xe2x80x9cInfectious Diseasexe2x80x9d, and xe2x80x9cRegenerationxe2x80x9d sections below, in Example 11, 19, and 20, and elsewhere herein. Briefly, the protein is useful in detecting, treating, and/or preventing congenital disorders (i.e. nevi, moles, freckles, Mongolian spots, hemangiomas, port-wine syndrome), integumentary tumors (i.e. keratoses, Bowen""s disease, basal cell carcinoma, squamous cell carcinoma, malignant melanoma, Paget""s disease, mycosis fungoides, and Kaposi""s sarcoma), injuries and inflammation of the skin (i.e. wounds, rashes, prickly heat disorder, psoriasis, dermatitis), atherosclerosis, uticaria, eczema, photosensitivity, autoimmune disorders (i.e. lupus erythematosus, vitiligo, dermatomyositis, morphea, scleroderma, pemphigoid, and pemphigus), keloids, striae, erythema, petechiae, purpura, and xanthelasma. In addition, such disorders may predispose increased susceptibility to viral and bacterial infections of the skin (i.e. cold sores, warts, chickenpox, molluscum contagiosum, herpes zoster, boils, cellulitis, erysipelas, impetigo, tinea, athletes foot, and ringworm).
Moreover, the protein product of this clone may also be useful for the treatment or diagnosis of various connective tissue disorders (i.e., arthritis, trauma, tendonitis, chrondomalacia and inflammation, etc.), autoimmune disorders (i.e., rheumatoid arthritis, lupus, scleroderma, dermatomyositis, etc.), dwarfism, spinal deformation, joint abnormalities, and chondrodysplasias (i.e. spondyloepiphyseal dysplasia congenita, familial osteoarthritis, Atelosteogenesis type II, metaphyseal chondrodysplasia type Schmid). Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:21 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 661 of SEQ ID NO:21, b is an integer of 15 to 675, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:21, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 12
Translation products corresponding to this gene share sequence homology with sodium hydrogen exchanger proteins(See, e.g., Genbank Accession AAC39643), which are thought to be involved in the electroneutral exchange of protons for Na+ and K+ across the mitochondrial inner membrane contributing to organelle volume and Ca2+ homeostasis Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with sodium hydrogen exchanger proteins. Such activities are known in the art, some of which are described elsewhere herein.
The polypeptide of this gene has been determined to have potential transmembrane domains at about amino acid position 19-35, 50-66, 158-174, 201-217, 235-251, 271-285, 320-336, 387-403, 430-446, and 456-472 of the amino acid sequence referenced in Table 1 for this gene. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type IIIb membrane proteins.
In a specific embodiment, polypeptides comprising the amino acid sequence of the open reading frame upstream of the predicted signal peptide are contemplated by the present invention. Specifically, polypeptides of the invention comprise, or alternatively consist of the following amino acid sequence:
In a further specific embodiment, polypeptides of the invention comprise, or alternatively consist of, the following amino acid sequence:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in germinal center B cell, and other cells of the immune system (e.g., thymus stromal cells, bone marrow stromal cells, dendritic cells and T cells) and to a lesser extent in stromal cells and brain.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: including arthritis, asthma, immunodeficiency diseases and leukemia. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 93 as residues: Leu-4 to Ser-18. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The homology of this gene to a sodium/hydrogen exchanger protein suggests that this gene is involved in cellular metabolism and maintaining Calcium homeostasis. The balance of calcium in the cell is extremely important with regards to signal transduction. Thus, expression of this gene in cells of the immune and nervous systems indicates that this gene may have a role in helping cells respond to extracellular signals to proliferate, differentiate, migrate, survive or die. Accordingly, the polynucleotides and/or polypeptides corresponding to this gene (and/or antibodies raised against those polypeptides) would be useful for treatment/detection of immune disorders such as arthritis, asthma, immune deficiency diseases such as AIDS, and leukemia, allergy, graft rejection, systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and other autoimmune conditions, infections, chronic variable immune deficiency (CVID) and other immune deficiency syndromes, respiratory distress syndrome and inflammation, neoplasms of the immune/hematopoietic system including leukemias, lymphomas and other proliferative disorders such as multiple myeloma, Hodgkin""s and non-Hodgkin""s lymphoma, and myelodypsplastic syndromes.
Further, the expression of this gene in the nervous system of the human indicates that the polynucleotides and/or polypeptides corresponding to this gene, (and/or antibodies raised against those polypeptides) are useful in the detection, diagnosis and treatment of neurological conditions such as manic depression, Alzheimer""s, Huntington""s, and Parkinson""s disease, Tourette""s syndrome and other neurodegenerative diseases including but not limited to, demyelinating diseases, epilepsy, headache, migraine, CNS infections, neurological trauma and neural regrowth following trauma, CNS neoplasms, stroke and reperfusion injury following stroke. It may also be useful for the treatment and diagnosis of learning and cognitive diseases, depression, dementia, pyschosis, mania, bipolar syndromes, schizophrenia and other psychiatric conditions. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
The polynucleotides and/or polypeptides corresponding to this gene (and/or antibodies raised against those polypeptides) would be useful for treatment/detection in the treatment/detection of thymus disorders such as Graves Disease, lymphocytic thyroiditis, hyperthyroidism and hypothyroidism; and in the treatment/detection of pineal gland disorders such as the circadian rhythm disturbances associated with shift work, jet lag, blindness, insomnia and old age.
Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:22 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1567 of SEQ ID NO:22, b is an integer of 15 to 1581, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:22, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 13
The translation product of this gene shares sequence homology with a novel protein with a calcium binding motif (See, e.g., Genbank Accession number J30027) which may be important in calcium mediated signaling events. Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with calcium binding proteins. Such activities are known in the art, some of which are described elsewhere herein.
In a specific embodiment, polypeptides comprising the amino acid sequence of the open reading frame upstream of the predicted signal peptide are contemplated by the present invention. Specifically, polypeptides of the invention comprise, or alternatively consist of the following amino acid sequence:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of, an amino acid sequence selected from the group consisting of:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in bone marrow stroma and arthritic bone and to a lesser extent in pregnant uterus, retina, brain, dendritic cells and several other tissues and cell lines.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: osteoporosis, osteoarthritis or other bone related diseases. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the skeletal system and blood forming tissues, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 94 as residues: Ala-24 to Pro-29, Asp-42 to Glu-50, Asp-81 to Asn-86, Lys-102 to Gln-108, Arg-126 to Tyr-135. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution and homology to calcium binding proteins suggests that the protein product of this clone would be useful for diagnosis, treatment and monitoring of diseases of the bone and joints including osteoporosis, osteoarthritis, bone cancers, and diseases of the bone marrow leading to alterations in the cells of the circulatory system. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:23 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 908 of SEQ ID NO:23, b is an integer of 15 to 922, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:23, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 14
The translation product of this gene appears to be the human homolog of a mouse interferon-gamma (IFN-g)-induced protein expressed in peritoneal macrophages (see GenBank accession AAA66219, and Lafuse et al. (J. Leukocyte Biol. 57(3):477-83). When tested against T-cells, polypeptides of the present invention stimulated IL-5 release.
It has been discovered that this gene is expressed in bone marrow, activated T-cells and monocytes, as well as in fetal tissues, placenta, infant brain, corneal stromal cells, and a number of cancerous tissues (including ovary and colon cancers, and T-cell lymphoma).
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: neurological, immune and hematopoietic disorders as well as developmental and proliferative disorders, including cancer. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune, hemopoietic and central nervous system, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., bone marrow, neural, immune, cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 95 as residues: Met-1 to Ala-28, Pro-40 to Glu-48, Ile-68 to Ile-73, Gly-183 to Glu-188, Pro-286 to Ser-295, Val-301 to Gly-307, Asp-311 to His-321. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution and homology to a mouse interferon-induced gene suggests that the protein product of this clone would be useful for treatment and diagnosis of disorders of the immune and hematopoietic systems, as well as neurological disorders, including epilepsy, Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. The expression of this gene in highly proliferative tissues (e.g. fetus, placental, infant brain, cancers) suggests that translation products of this gene may be involved in cell differentiation and/or proliferation. Therefore, protein, as well as antibodies directed against the protein, may show utility as tumor markers and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:24 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2274 of SEQ ID NO:24, b is an integer of 15 to 2288, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:24, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 15
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 3-19 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 20-81 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ib membrane proteins.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in colon and to a lesser extent in prostate, dendritic cells, healing groin wound, keratinocytes, and ovary.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: gastrointestinal system, colorectal cancer, reproductive system. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the gastrointestinal system, reproductive and immune system expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., immune, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 96 as residues: Thr-22 to Cys-40, Val-44 to His-56. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in colon, colon cancer and ovary tumor indicates that polynucleotides and polypeptides corresponding to this gene are useful for diagnosis, treatment and/or detection of tumors, especially of the intestine, such as, carcinoid tumors, lymphomas, cancer of the colon and cancer of the rectum, as well as cancers of the ovary and other tissues where the expression has been indicated. The expression in the colon and ovary tissues, and immune cells may indicate the gene or its products can be used to treat and/or diagnose other disorders of the gastrointestinal, reproductive, and immune including inflammatory disorders such as, diverticular colon disease (DCD), inflammatory colonic disease, Crohn""s disease (CD), non-inflammatory bowel disease (non-IBD) colonic inflammation; ulcerative disorders such as, ulcerative colitis (UC), amebic colitis, eosinophilic colitis; non-cancerous tumors, such as, polyps in the colon, adenomas, leiomyomas, lipomas, and angiomas. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:25 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 894 of SEQ ID NO:25, b is an integer of 15 to 908, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:25, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 16
This gene is expressed primarily in developing lung, hemangiopericytoma and merkel cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: disorders of the skin, peripheral neuropathy, diseases of the lung, and cancers, particularly of the connective tissues (for example, involving pericytes) and soft tissues. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the skin, pulmonary, and peripheral nervous systems, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., pulmonary, cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 97 as residues: Ala-55 to Ser-60. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in Merkel cells indicates that polynucleotides and polypeptides corresponding to this gene are useful for treatment of disorders involving sensory innervation such as peripheral neuropathy and sensory loss associated with leprosy. Moreover, the protein product of this clone is useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
Alternatively, the protein is useful for the treatment of disorders involving loss of lung function such as emphysema, ARDS, and cystic fibrosis. The protein is also useful for the treatment, detection, and/or prevention of pain disorders. The tissue distribution in Merkel cells also indicates that polynucleotides and polypeptides corresponding to this gene are useful for treatment of disorders involving: the skin (particularly, but not limited to, skin cancer); the lungs (for example lung cancer); and pericytes (particularly, but not limited to, hemangiopericytoma). Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:26 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2076 of SEQ ID NO:26, b is an integer of 15 to 2090, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:26, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 17
A supernatant from a transfection of this gene has been shown to induce transcription in Jurkat T-cells by the SEAP assay. Specifically, when tested against Jurkat T-cell lines, supernatants removed from cells containing this gene activated the GAS (gamma activating sequence) promoter element. Thus, it is likely that this gene activates T-cells, and to a lesser extent, in immune and hematopoietic cells and tissue cell types, through the Jak-Stat signal transduction pathway. GAS is a promoter element found upstream of many genes which are involved in the Jak-STAT pathway. The Jak-STAT pathway is a large, signal transduction pathway involved in the differentiation and proliferation of cells. Therefore, activation of the Jak-STAT pathway, reflected by the binding of the GAS element, can be used to indicate proteins involved in the proliferation and differentiation of cells.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in neurological tissue (including cerebellum, adult brain, epileptic frontal cortex, corpus colosum, and fetal brain) and to a lesser extent in T-cells and other immunological tissues, as well as a variety of tumors and other normal adult and fetal tissues.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: neural diseases and/or disorders, particularly cancer and other proliferative disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the neurological and immune systems, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, immune, hematopoietic, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 98 as residues: Thr-52 to Phe-62, Pro-130 to Arg-135, Pro-160 to Arg-173, Thr-190 to His-195, Gly-246 to Arg-252, Arg-397 to Thr-403, Gly-414 to Arg-420, Arg-483 to Glu-488. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in neurological tissue indicates that polynucleotides and polypeptides corresponding to this gene are useful for diagnosis and treatment of cancer and other proliferative disorders, particularly of neural and immune tissues. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:27 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2341 of SEQ ID NO:27, b is an integer of 15 to 2355, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:27, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 18
Supernatants from cells expressing this gene stimulate T cells and or NK cells to secrete interferon-gamma. Interferon gamma is an immunomodulatory cytokine that, for example, regulates inflammation and inhibits Th2 immune responses.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of, an amino acid sequence selected from the group consisting of:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in glioblastoma and fetal tissues (including fetal heart, fetal lung and fetal liver/spleen) and to a lesser extent in retina, germinal center B cells (from chronic lymphocytic leukemia and germinal center), and apoptotic T-cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: neural, developmental, and immune diseases and/or disorders, particularly cancer and other proliferative disorders, including glioblastoma. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the brain and fetal tissues, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, developmental, immune, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
The tissue distribution in neural tissues indicates that polynucleotides and polypeptides corresponding to this gene are useful for diagnosis and treatment of cancer and other proliferative disorders, particularly of the brain and fetal tissue. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Alternatively, the expression within developmental tissues indicates that the protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions.
Additionally, the homology of the ability of this gene to stimulate the secretion of interferon-gamma indicates that the polynucleotides and/or polypeptides corresponding to this gene (and/or antibodies raised against those polypeptides) are useful for the diagnosis and treatment of diseases and disorders associated with the immune system, including, but not limited to, allergy, asthma, graft rejection, systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and other autoimmune conditions, infections, AIDS, chronic variable immune deficiency (CVID) and other immune deficiency syndromes, respiratory distress syndrome and inflammation, neoplasms of the immune/hematopoietic system including leukemias, lymphomas and other proliferative disorders such as multiple myeloma, Hodgkin""s and non-Hodgkin""s lymphoma, and myelodypsplastic syndromes. The polynucleotides and/or polypeptides corresponding to this gene (and/or antibodies raised against those polypeptides) may also be useful for stimulating the immune response to bolster the immune response to diseases such as cancer or infection.
Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:28 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1666 of SEQ ID NO:28, b is an integer of 15 to 1680, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:28, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 19
Contact of MVEC cells with supernatant expressing the product of this gene was shown to increase the expression of a soluble adhesion molecule, specifically, ICAM-1. Thus it is likely that the product of this gene is involved in the activation of MVEC, in addition to other endothelial cell-lines or tissue cell types. Thus, polynucleotides and polypeptides related to this gene have uses which include, but are not limited to, activating vascular endothelial cells, such as during an inflammatory response.
The polypeptide encoded by this gene has been determined to have a transmembrane domain at about amino acid position 61 to about 77 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing about amino acids 1 to about 60 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type II membrane proteins.
It has been discovered that this gene is expressed primarily in Soares infant brain 1NIB and to a lesser extent in normalized infant brain cDNA.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: neurodevelopmental and/or neurodegenerative diseases or disorders. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the central nervous system, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., nervous, neural, neuronal, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, lymph, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 100 as residues: Leu-27 to Glu-32. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in fetal brain indicates that polynucleotides and/or polypeptides corresponding to this gene would be useful for the detection, diagnosis, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, diagnosis, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception.
In addition, elevated expression of polynucleotides and/or polypeptides corresponding to this gene in regions of the brain indicates that polynucleotides and/or polypeptides of the invention may play a role in normal neural function. Potentially, polynucleotides and/or polypeptides of the invention are involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
The predicted membrane localization indicates that polynucleotides and/or polypeptides corresponding to this gene would be a good target for antagonists, particularly small molecules or antibodies, which block functional activity (such as, for example, binding of the receptor by its cognate ligand(s); transport function; signaling function). Accordingly, preferred are antibodies and or small molecules which specifically bind an extracellular portion of the translation product of this gene. The extracellular regions can be ascertained from the information regarding the transmembrane domains as set out above. Also provided is a kit for detecting tumors in which expression of polynucleotides and/or polypeptides corresponding to this gene occurs. Such a kit comprises in one embodiment an antibody specific for polynucleotides and/or polypeptides corresponding to this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:29 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1604 of SEQ ID NO:29, b is an integer of 15 to 1618, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:29, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 20
The translation product of this gene shares sequence homology with, and is believed to be a novel homolog of, GDNF. GDNF, neurturin (see, e.g., Genbank Accession No. gb|AAC50898.1|; all references available through this accession are hereby incorporated in their entirety by reference herein), persephin (see, e.g., Genbank Accession No. gb|AAC39640.1|(AF040962); all references available through this accession are hereby incorporated in their entirety by reference herein) and related family members serve useful roles as survival factors for neurons, particularly dopaminergic neurons. They can also have neurotrophic effects on neurons. GDNF and Neurturin (NTN) can each activate the MAP kinase signaling pathway in cultured sympathetic neurons and support the survival of sympathetic neurons, as well as of sensory neurons and dorsal root ganglia. Persephin, like GDNF and NTN, promotes the survival of ventral midbrain dopaminergic neurons in culture and prevents their degeneration after 6-hydroxydopamine treatment in vivo. Persephin also supports the survival of motor neurons in culture and in vivo after sciatic nerve axotomy and, like GDNF, promotes ureteric bud branching. However, in contrast to GDNF and NTN, persephin does not support peripheral neurons. Fibroblasts transfected with Ret and one of the coreceptors GFRalpha-1 or GFRalpha-2 do not respond to persephin, suggesting that persephin utilizes additional, or different, receptor components than GDNF and NTN. For these reasons, they may play key roles in mediating outcome of neurodegenerative disorders, such asamyotrophic lateral sclerosis (ALS) and Parkinson""s disease. Potentially, it may turn out that GDNF-like molecules (i.e., novel family members) will exert survival, proliferation, or trophic effects on other cell types besides neurons. Thus, based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with GDNF family member proteins. Such activities are known in the art, some of which are described elsewhere herein.
It has been discovered that this gene is expressed primarily in smooth muscle.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: neural and vascular diseases and/or disorders. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the CNS, PNS, and vascular systems, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., vascular, neural, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 101 as residues: Pro-75 to Cys-84. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The homology to GDNF indicates that polynucleotides and/or polypeptides corresponding to this gene would be useful for the detection, diagnosis, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, diagnosis, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Moreover, the protein is useful in the detection, treatment, and/or prevention of a variety of vascular disorders and conditions, which include, but are not limited to microvascular disease, vascular leak syndrome, aneurysm, stroke, embolism, thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:30 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 959 of SEQ ID NO:30, b is an integer of 15 to 973, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:30, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 21
The translation product of this clone shares sequence homology to the NADH oxidoreductase complex I subunit of Caenorhabditis elegans (See Genbank Accession No. gi|5019819|gb|AAD37863.1|AF143152xe2x80x941 and Nucleic Acids Res. 27 (17), 3424-3432 (1999); all information contained within this accession and publication is hereby incorporated herein by reference). Based on the sequence similarity, the translation product of this clone is expected to share at least some biological activities with NADH oxidoreductase proteins. Such activities are known in the art, some of which are described elsewhere herein.
The polypeptide of this gene has been determined to have five transmembrane domains at about amino acid position 62-78, 95-111, 113-129, 149-65, and 169-185 of the amino acid sequence referenced in Table 1 for this gene. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type IIIa membrane proteins.
A preferred polypeptide fragment of the invention comprises the following amino acid sequence:
Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in fetal liver spleen and to a lesser extent in most tissues and/or cell types examined.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: hematopoietic and immune diseases and/or disorders, particularly multiple myeloma, leukemia, and hemophilia. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune and hematopoietic systems, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., hematopoietic, immune, developmental, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 102 as residues: Gly-88 to Arg-93, Ser-133 to Tyr-138, Phe-189 to Gly-195, Thr-211 to Gly-227. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution enrichment in fetal liver spleen indicates that polynucleotides and polypeptides corresponding to this gene are useful for the treatment and/or detection of immune and/or hematopoietic disorders including arthritis, asthma, immunodeficiency diseases, leukemia, transplant rejection, and microbial infections. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Additionally this gene""s homology to the NADH oxidoreductase complex I subunit protein indicates that this gene may play a role in cellular metabolism. Thus, the polynucleotides and/or polypeptides corresponding to this gene (and/or antibodies raised against those polypeptides) may be useful in detecting, diagnosing, and or treating complex I deficiencies. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:31 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1175 of SEQ ID NO:31, b is an integer of 15 to 1189, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:31, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 22
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, an amino acid sequence selected from the group:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in Soares adult brain N2b4HB55Y and to a lesser extent in epididymus, soares testis NHT, macrophage, and dendritic cells, placenta, tonsils, helper T-cells, embryo, and amniotic cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: neurodegenerative and immune disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the central nervous system and immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, immune, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 103 as residues: Tyr-2 to Trp-7, Arg-42 to Thr-50. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in brain indicates the protein product of this clone is useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
The tissue distribution in immune cells (e.g., T-cells and macrophage) indicates the protein product of this clone is useful for the diagnosis and treatment of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:32 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1898 of SEQ ID NO:32, b is an integer of 15 to 1912, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:32, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 23
The translation product of this gene shares sequence homology with zinc finger proteins (see, e.g., Genbank Accession numbers CAA17278.1 and AAC51180; all references available through this accession are hereby incorporated by reference herein.). Additionally, the translation product of this gene shares sequence homology with OTIC 18 brain-specific nucleosome assembly protein and BRCA1-associated protein (see, e.g., Genseq accession numbers W37504 and W52187, respectively) which are important for diagnosis or therapy of hereditary disease and cancers, particularly of the brain, ovaries, and breast.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, an amino acid sequence selected from the group:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides) are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in brain frontal cortex, ovary, skin, dendritic cells, skin, bone marrow and to a lesser extent in colon.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: ovarian cancer, brain cancer, neurodegenerative and immune disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the central nervous system, ovaries, colon, and immune cells, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., immune, ovarian, neural, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
The tissue distribution in brain and homology to OTIC 18 indicates the protein product of this clone is useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, inflammatory conditions, or brain cancer. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. The tissue distribution in ovaries and homology to BRCA1-associated protein indicates that polynucleotides and polypeptides corresponding to this gene are useful for detection, treatment, and/or prevention of ovarian and/or breast cancer.
The tissue distribution in bone marrow and dendritic cells indicates the protein product of this clone is useful for the diagnosis and treatment of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:33 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2380 of SEQ ID NO:33, b is an integer of 15 to 2394, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:33, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 24
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 2-18 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 19-49 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ib membrane proteins.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of this polypeptide (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridize, under stringent conditions, to the polynucleotide encoding this polypeptide are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding this polypeptide are also encompassed by the invention.
This gene is expressed primarily in brain frontal cortex
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: neurological conditions. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the nervous system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
The tissue distribution in brain indicates the protein product of this clone is useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:34 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 2104 of SEQ ID NO:34, b is an integer of 15 to 2118, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:34, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 25
The translation product of this gene shares sequence homology with Alix from Mus musculus, which is thought to be important in activation of apoptosis. According to Vito, et. al, J.Biol Chem (1999) Mouse ALIX (or AIP1 according to the authors"" nomenclature) interacts with ALG-2 and is required for the calcium dependent step of apoptosis.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of the following amino acid sequence selected from the group consisting of:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
The gene encoding the disclosed cDNA is believed to reside on chromosome 3. Accordingly, polynucleotides related to this invention are useful as a marker in linkage analysis for chromosome 3.
This gene is expressed primarily in prostate cancer, osteoblasts, microvascular endothelial cells, umbilical vein, breast, fetal cochlea, pancreas tumor, fetal heart, testes, 8 week whole embryo, fetal liver spleen, and primary dendritic cells and to a lesser extent in a variety of normal and transformed adult and fetal tissues and cell lines.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: vascular, hematopoietic, reproductive, and developmental diseases and/or disorders, particularly cancer and other proliferative disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the prostate skeletal system, breast, pancreas, testes, and the immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., vascular, hematopoietic, and developmental, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, amniotic fluid, seminal fluid, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 106 as residues: Thr-28 to Gln-36, Gln-138 to Gly-145. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in microvascular endothelial cells and umbilical vein, combined with the homology to the Alix protein, a factor which is required for apoptosis, indicates that polynucleotides and polypeptides corresponding to this gene are useful for treatment and diagnosis of cancer and other proliferative disorders, especially prostate cancer, since such a protein product could potentially be used to induce programmed cell death in tumors. Moreover, this protein may represent a protein which is constitutively down regulated in proliferative cells and tissues, and primarily in vascular tissues. Thus, agonizes of this protein may inhibit vascularization in tumors by returning the cellular control of this protein to basal, non-transformed levels. Moreover, the protein is useful in the detection, treatment, and/or prevention of a variety of vascular disorders and conditions, which include, but are not limited to microvascular disease, vascular leak syndrome, aneurysm, stroke, embolism, thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:35 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 6051 of SEQ ID NO:35, b is an integer of 15 to 6065, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:35, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 26
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 13-29 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 30-56 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ia membrane proteins.
This gene is expressed primarily in fetal tissue (e.g., liver, spleen), prostate, brain, colon, bone marrow and T-cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: developmental, immune, and neurodegenerative disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the central nervous system and immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., neural, immune, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 107 as residues: Thr-39 to Leu-53. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in brain indicates the protein product of this clone is useful for the detection, treatment, and/or prevention of neurodegenerative disease states, behavioral disorders, or inflammatory conditions. Representative uses are described in the xe2x80x9cRegenerationxe2x80x9d and xe2x80x9cHyperproliferative Disordersxe2x80x9d sections below, in Example 11, 15, and 18, and elsewhere herein. Briefly, the uses include, but are not limited to the detection, treatment, and/or prevention of Alzheimer""s Disease, Parkinson""s Disease, Huntington""s Disease, Tourette""s Syndrome, meningitis, encephalitis, demyelinating diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, depression, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, elevated expression of this gene product in regions of the brain indicates it plays a role in normal neural function. Potentially, this gene product is involved in synapse formation, neurotransmission, learning, cognition, homeostasis, or neuronal differentiation or survival.
The tissue distribution in immune cells (e.g., T-cells) and bone marrow indicates the protein product of this clone is useful for the diagnosis and treatment of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types.
Moreover, the expression within fetal tissue and other cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation. Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA). Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus this protein may modulate apoptosis or tissue differentiation and would be useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:36 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1351 of SEQ ID NO:36, b is an integer of 15 to 1365, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:36, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 27
This invention relates to newly identified Lipocolon polynucleotides, polypeptides encoded by such polynucleotides, the use of such polynucleotides and polypeptides, as well as the production of such polynucleotides and polypeptides. The polypeptide of the present invention has been putatively identified as a human lipocalin homolog derived from colon carcinoma cDNA library. More particularly, the polypeptide of the present invention has been putatively identified as a human lipocalin colon carcinoma-derived protein, sometimes hereafter referred to as xe2x80x9cLipocolonxe2x80x9d and/or xe2x80x9cLPCxe2x80x9d. The invention also relates to inhibiting the action of such polypeptides.
The lipocalin protein family is a large group of small extracellular proteins. The family demonstrates great diversity at the sequence level, though most lipocalins share three characteristic conserved sequence motifs. The kernel lipocalins represent a more divergent family member as they share only a single conserved sequence motif. Belying this sequence dissimilarity, lipocalin crystal structures are highly conserved and comprise a single eight-stranded continuously hydrogen-bonded anti-parallel beta-barrel, which encloses an internal ligand-binding site. Together with two other families of ligand-binding proteins, the fatty-acid-binding proteins (FABPs) and the avidins, the lipocalins form part of an overall structural superfamily: the calycins.
Members of the lipocalin family are characterized by several common molecular-recognition properties: the ability to bind a range of small hydrophobic molecules, binding to specific cell-surface receptors and the formation of complexes with soluble macromolecules. The varied biological functions of the lipocalins are mediated by one or more of these properties. In the past, the lipocalins have been classified as transport proteins; however, it is now clear that the lipocalins exhibit great functional diversity, with roles in retinol transport, invertebrate cryptic coloration, olfaction and pheromone transport, and prostaglandin synthesis. These general properties suggest such proteins as appropriate transporters transferring biologically hazardous molecules in a safe and controlled manner between cells. Moreover, many lipocalins have been implicated in the regulation of cell homeostasis: apolipoprotein D, quiescience specific protein, purpurin, alpha-1-microglobulin, and NGAL. This combination of direct and indirect evidence indicates that the lipocalin protein family is involved, in a quite general way, in the mediation of cell regulation and that many presently functionless family members might act in this way.
The lipocalins have also been implicated in the regulation of cell homoeostasis and the modulation of the immune response, and, as carrier proteins, to act in the general clearance of endogenous and exogenous compounds. Roles for lipocalins in cell regulation have been proposed. Recently, NGAL (Neutrophil gelatinase-associated lipocalin) has been attributed to the pathogenesis of certain pathologic conditions in the colonic mucosa (See Nielsen BS, et al., Gut Mar;38(3):414-20; which is hereby incorporated herein). Interestingly, NGAL was found in a variety of normal and pathological human tissues. Neoplastic human tissues showed a very heterogeneous expression of NGAL protein. High NGAL levels were found in adenocarcinomas of lung, colon and pancreas. In contrast, renal cell carcinomas of various subtypes and prostate cancers contained low NGAL levels. Lymphomas and thymic tumors were negative for NGAL immuno-labeling.
Certain lipocalins are able to induce strong allergic responses. The molecular mimicry between lipocalin allergens and endogenous lipocalins at the T-cell level may explain why the immune response against lipocalins is Th2-dominated and results in allergy. This view is supported by recent studies of autoimmune and parasitic diseases and peptide analogues. The literature has intriguing references to members of the lipocalin family. For example, experiments have shown that the serum measurement of a protein from the neutrophil, human neutrophil lipocalin (HNL), is a superior means to distinguish acute bacterial and viral infections. Prostaglandin (PG) D2 is recognized as the most potent endogenous sleep-promoting substance whose action mechanism is the best characterized among the various sleep-substances thus far reported. Lipocalin-type PGD synthase is dominantly produced in the arachnoid membrane and choroid plexus of the brain, and is secreted into the CSF to become beta-trace, a major protein component of the CSF. The PGD synthase as well as the PGD2 thus produced circulates in the ventricular system, subarachnoidal space, and extracellular space in the brain system. PGD2 then interacts with DP receptors in the chemosensory region of the ventro-medial surface of the rostral basal forebrain to initiate the signal to promote sleep probably via the activation of adenosine A2A receptive neurons.
The polypeptide of the present invention has been putatively identified as a member of the lipocalin family and has been termed Lipocolon (xe2x80x9cLPCxe2x80x9d). This identification has been made as a result of amino acid sequence homology to lipocalin of Bufo marinus, prostaglandin D synthase, and cpl-1 proteins of Xenopus laevis, in combination with its isolation from a human colon carcinoma cDNA library.
FIG. 1 shows the nucleotide (SEQ ID NO:37) and deduced amino acid sequence (SEQ ID NO:201) of LPC. Predicted amino acids from about 48 to about 62 constitute the predicted lipocalin motif II (amino acid residues from about 48 to about 62 in SEQ ID NO:201) and are represented by the underlined amino acid regions; amino acids from about 77 to about 92 constitute the lipocalin motif III (amino acid residues from about 77 to about 92 in SEQ ID NO:201) and are represented by the double underlined amino acids.
FIG. 2 shows the regions of similarity between the amino acid sequences of the Lipocolon (LPC) protein (SEQ ID NO:201), the lipocalin of Bufo marinus, emb|CAA48138.1 (SEQ ID NO: 202); the Xenopus prostaglandin D synthase, dbj|BAA12075.1 (SEQ ID NO: 203); and the Xenopus cpl-1 proteins, emb|CAA59132.1 (SEQ ID NO: 204).
FIG. 3 shows an analysis of the Lipocolon (LPC) amino acid sequence. Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity; amphipathic regions; flexible regions; antigenic index and surface probability are shown.
A polynucleotide encoding a polypeptide of the present invention is obtained from human colon adenocarcinoma, colon carcinoma, and cervical adenocarcinoma tissues, in addition to HeLa S3 cell line cells. The polynucleotide of this invention was discovered in a human colon carcinoma cDNA library. Its translation product has homology to the characteristic lipocalin domains. As shown in FIG. 1 and FIG. 2, LCP has two lipocalin domains (the lipocalin domains comprise amino acids 48-62 and/or 77-92 of SEQ ID NO:201; which correspond to amino acids 48 xc3x1 62 and/or 77-92 of FIG. 1) with strong conservation between other members of the lipocalin family. The polynucleotide contains an open reading frame encoding a portion of the LPC polypeptide of 123 amino acids. LCP exhibits a high degree of homology at the amino acid level to the lipocalin of Bufo marinus, prostaglandin D synthase and cpl-1 proteins of Xenopus laevis (as shown in FIG. 2).
The present invention provides isolated nucleic acid molecules comprising a polynucleotide encoding the LCP polypeptide having the amino acid sequence shown in FIG. 1 (SEQ ID NO:201), which was determined by sequencing a cloned cDNA, gene HWNFG66. The nucleotide sequence shown in FIG. 1 (SEQ ID NO:37) was obtained by sequencing a cDNA gene (HWNFG66), which was deposited on Sep. 27, 1999 at the American Type Culture Collection, and given Accession Number PTA-797. The deposited gene (HWNFG66) is inserted in the pSport plasmid (Life Technologies, Rockville, Md.) using the SalI/NotI restriction endonuclease cleavage sites.
The present invention is further directed to fragments of the isolated nucleic acid molecules described herein. By a fragment of an isolated DNA molecule having the nucleotide sequence of the deposited cDNA or the nucleotide sequence shown in SEQ ID NO:37 is intended DNA fragments at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt in length which are useful as diagnostic probes and primers as discussed herein. Of course, larger fragments 50-1500 nt in length are also useful according to the present invention, as are fragments corresponding to most, if not all, of the nucleotide sequence of the deposited cDNA or as shown in SEQ ID NO:37. By a fragment at least 20 nt in length, for example, is intended fragments which include 20 or more contiguous bases from the nucleotide sequence of the deposited cDNA or the nucleotide sequence as shown in SEQ ID NO:37 (FIG. 1). In this context xe2x80x9caboutxe2x80x9d includes the particularly recited size, larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini.
Representative examples of LCP polynucleotide fragments of the invention include, for example, fragments that comprise, or alternatively, consist of, a sequence from about nucleotide 1 to about 50, from about 51 to about 100, from about 101 to about 150, from about 151 to about 200, from about 201 to about 250, from about 251 to about 300, from about 301 to about 350, from about 351 to about 400, from about 401 to about 450, from about 451 to about 500, from about 501 to about 550, from about 551 to about 570, from about 1 to about 236, from about 144 to about 188, from about 231 to about 276 of SEQ ID NO:37 (FIG. 1), or the complementary strand thereto, or the cDNA contained in the deposited gene. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini.
Preferred nucleic acid fragments of the present invention include nucleic acid molecules encoding a member selected from the group: a polypeptide comprising or alternatively, consisting of, any one of the lipocalcin domains (amino acid residues from about 48 to about 62 and/or 77 to about 92 in FIG. 1 (amino acids from about 48 to about 62 and/or 77 to about 92 in SEQ ID NO:201). Since the location of these domains have been predicted by computer analysis, one of ordinary skill would appreciate that the amino acid residues constituting these domains may vary slightly (e.g., by about 1 to 15 amino acid residues) depending on the criteria used to define each domain.
In additional embodiments, the polynucleotides of the invention encode functional attributes of LCP. Preferred embodiments of the invention in this regard include fragments that comprise alpha-helix and alpha-helix forming regions (xe2x80x9calpha-regionsxe2x80x9d), beta-sheet and beta-sheet forming regions (xe2x80x9cbeta-regionsxe2x80x9d), turn and turn-forming regions (xe2x80x9cturn-regionsxe2x80x9d), coil and coil-forming regions (xe2x80x9ccoil-regionsxe2x80x9d), hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions and high antigenic index regions of LCP.
The data representing the structural or functional attributes of LCP set forth in FIG. 3 and/or Table 8, as described above, was generated using the various modules and algorithms of the DNA*STAR set on default parameters. In a preferred embodiment, the data presented in columns VIII, IX, XIII, and XIV of Table 8 can be used to determine regions of LCP which exhibit a high degree of potential for antigenicity. Regions of high antigenicity are determined from the data presented in columns VIII, IX, XIII, and/or XIV by choosing values which represent regions of the polypeptide which are likely to be exposed on the surface of the polypeptide in an environment in which antigen recognition may occur in the process of initiation of an immune response.
Certain preferred regions in these regards are set out in FIG. 3, but may, as shown in Table 8, be represented or identified by using tabular representations of the data presented in FIG. 3. The DNA*STAR computer algorithm used to generate FIG. 3 (set on the original default parameters) was used to present the data in FIG. 3 in a tabular format (See Table 8). The tabular format of the data in FIG. 3 is used to easily determine specific boundaries of a preferred region.
The above-mentioned preferred regions set out in FIG. 3 and in Table 8 include, but are not limited to, regions of the aforementioned types identified by analysis of the amino acid sequence set out in FIG. 1. As set out in FIG. 3 and in Table 8, such preferred regions include Garnier-Robson alpha-regions, beta-regions, turn-regions, and coil-regions, Chou-Fasman alpha-regions, beta-regions, and turn-regions, Kyte-Doolittle hydrophilic regions and Hopp-Woods hydrophobic regions, Eisenberg alpha- and beta-amphipathic regions, Karplus-Schulz flexible regions, Jameson-Wolf regions of high antigenic index and Emini surface-forming regions.
Even if deletion of one or more amino acids from the N-terminus of a protein results in modification of loss of one or more biological functions of the protein, other functional activities (e.g., biological activities, ability to multimerize, etc.) may still be retained. For example, the ability of shortened LCP muteins to induce and/or bind to antibodies which recognize the complete or mature forms of the polypeptides generally will be retained when less than the majority of the residues of the complete or mature polypeptide are removed from the N-terminus. Whether a particular polypeptide lacking N-terminal residues of a complete polypeptide retains such immunologic activities can readily be determined by routine methods described herein and otherwise known in the art. It is not unlikely that an LCP mutein with a large number of deleted N-terminal amino acid residues may retain some biological or immunogenic activities. In fact, peptides composed of as few as six LCP amino acid residues may often evoke an immune response.
Accordingly, the present invention further provides polypeptides having one or more residues deleted from the amino terminus of the LCP amino acid sequence shown in FIG. 1, up to the proline residue at position number 117 and polynucleotides encoding such polypeptides. In particular, the present invention provides polypeptides comprising the amino acid sequence of residues n1-123 of FIG. 1, where n1 is an integer from 2 to 117 corresponding to the position of the amino acid residue in FIG. 1 (which is identical to the sequence shown as SEQ ID NO:201).
In another embodiment, N-terminal deletions of the LCP polypeptide can be described by the general formula n2-123, where n2 is a number from 2 to 117, corresponding to the position of amino acid identified in FIG. 1. N-terminal deletions of the LCP polypeptide of the invention shown as SEQ ID NO:201 (FIG. 1) include polypeptides comprising, or alternatively consisting of, the amino acid sequence of residues: I-2 to P-117; R-3 to P-117; P-4 to P-117; T-5 to P-117; E-6 to P-117; E-7 to P-117; G-8 to P-117; G-9 to P-117; L-10 to P-117; H-11 to P-117; V-12 to P-117; H-13 to P-117; M-14 to P-117; E-15 to P-117; F-16 to P-117; P-17 to P-117; G-18 to P-117; A-19 to P-117; D-20 to P-117; G-21 to P-117; C-22 to P-117; N-23 to P-117; Q-24 to P-117; V-25 to P-117; D-26 to P-117; A-27 to P-117; E-28 to P-117; Y-29 to P-117; L-30 to P-117; K-31 to P-117; V-32 to P-117; G-33 to P-117; S-34 to P-117; E-35 to P-117; G-36 to P-117; H-37 to P-117; F-38 to P-117; R-39 to P-117 V-40 to P-117; P-41 to P-117; A-42 to P-117; L-43 to P-117; G-44 to P-117; Y-45 to P-117; L-46 to P-117; D-47 to P-117; V-48 to P-117; R-49 to P-117; I-50 to P-117; V-51 to P-117; D-52 to P-117; T-53 to P-117; D-54 to P-117; Y-55 to P-117; S-56 to P-117; S-57 to P-117; F-58 to P-117; A-59 to P-117; V-60 to P-117; L-61 to P-117; Y-62 to P-117; I-63 to P-117; Y-64 to P-117; K-65 to P-117; E-66 to P-117; L-67 to P-117; E-68 to P-117; G-69 to P-117; A-70 to P-117; L-71 to P-117; S-72 to P-117; T-73 to P-117; M-74 to P-117; V-75 to P-117; Q-76 to P-117; L-77 to P-117; Y-78 to P-117; S-79 to P-117; R-80 to P-117; T-81 to P-117; Q-82 to P-117; D-83 to P-117; V-84 to P-117; S-85 to P-117; P-86 to P-117; Q-87 to P-117; A-88 to P-117; L-89 to P-117; K-90 to P-117; A-91 to P-117; F-92 to P-117; Q-93 to P-117; D-94 to P-117; F-95 to P-117; Y-96 to P-117; P-97 to P-117; T-98 to P-117; L-99 to P-117; G-100 to P-117; L-101 to P-117; P-102 to P-117; E-103 to P-117; D-104 to P-117; M-105 to P-117; M-106 to P-117; V-107 to P-117; M-108 to P-117; L-109 to P-117; P-110 to P-117; Q-111 to P-117; or S-112 to P-117; of SEQ ID NO:201 (FIG. 1). Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that these bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Also as mentioned above, even if deletion of one or more amino acids from the C-terminus of a protein results in modification or loss of one or more biological functions of the protein, other functional activities (e.g., biological activities (e.g., ability to illicit mitogenic activity, induce differentiation of normal or malignant cells, bind to retinal, bind to retinoic acid, ability to bind small lipophilic molecules, etc.), ability to multimerize, ability to bind small lipophilic molecules receptors may still be retained. For example the ability of the shortened LCP mutein to induce and/or bind to antibodies which recognize the complete or mature forms of the polypeptide generally will be retained when less than the majority of the residues of the complete or mature polypeptide are removed from the C-terminus. Whether a particular polypeptide lacking C-terminal residues of a complete polypeptide retains such immunologic activities can readily be determined by routine methods described herein and otherwise known in the art. It is not unlikely that an LCP mutein with a large number of deleted C-terminal amino acid residues may retain some biological or immunogenic activities. In fact, peptides composed of as few as six LCP amino acid residues may often evoke an immune response.
Accordingly, the present invention further provides polypeptides having one or more residues deleted from the carboxy terminus of the amino acid sequence of the LCP polypeptide shown in FIG. 1, up to the glutamine residue at position number 7, and polynucleotides encoding such polypeptides. In particular, the present invention provides polypeptides comprising the amino acid sequence of residues 1-m1 of FIG. 1, where m1 is an integer from 7 to 117 corresponding to the position of the amino acid residue in FIG. 1.
Moreover, the invention provides polynucleotides encoding polypeptides comprising, or alternatively consisting of, the amino acid sequence of C-terminal deletions of the LCP polypeptide of the invention shown as SEQ ID NO:201 (FIG. 1) include polypeptides comprising the amino acid sequence of residues: A-1 to N-116; A-1 to C-115; A-1 to A-114; A-1 to D-113; A-1 to S-112; A-1 to Q-111; A-1 to P-110; A-1 to L-109; A-1 to M-108; A-1 to V-107; A-1 to M-106; A-1 to M-105; A-1 to D-104; A-1 to E-103; A-1 to P-102; A-1 to L-101; A-1 to G-100; A-1 to L-99; A-1 to T-98; A-1 to P-97; A-1 to Y-96; A-1 to F-95; A-1 to D-94; A-1 to Q-93; A-1 to F-92; A-1 to A-91; A-1 to K-90; A-1 to L-89; A-1 to A-88; A-1 to Q-87; A-1 A-1 to P-86; A-1 to S-85; A-1 to V-84; A-1 to D-83; A-1 to Q-82; A-1 to T-81; A-1 to R-80; A-1 to S-79; A-1 to Y-78; A-1 to L-77; A-1 to Q-76; A-1 to V-75; A-1 to M-74; A-1 to T-73; A-1 to S-72; A-1 to L-71; A-1 to A-70; A-1 to G-69; A-1 to E-68; A-1 to L-67; A-1 to E-66; A-1 to K-65; A-1 to Y-64; A-1 to I-63; A-1 to Y-62; A-1 to L-61; A-1 to V-60; A-1 to A-59; A-1 to F-58; A-1 to S-57; A-1 to S-56; A-1 to Y-55; A-1 to D-54; A-1 to T-53; A-1 to D-52; A-1 to V-51; A-1 to I-50; A-1 to R-49; A-1 to V-48; A-1 to D-47; A-1 to L-46; A-1 to Y-45; A-1 to G-44; A-1 to L-43; A-1 to A-42; A-1 to P-41; A-1 to V-40; A-1 to R-39; A-1 to F-38; A-1 to H-37; A-1 to G-36; A-1 to E-35; A-1 to S-34; A-1 to G-33; A-1 to V-32; A-1 to K-31; A-1 to L-30; A-1 to Y-29; A-1 to E-28; A-1 to A-27; A-1 to D-26; A-1 to V-25; A-1 to Q-24; A-1 to N-23; A-1 to C-22; A-1 to G-21; A-1 to D-20; A-1 to A-19; A-1 to G-18; A-1 to P-17; A-1 to F-16; A-1 to E-15; A-1 to M-14; A-1 to H-13; A-1 to V-12; A-1 to H-1; A-1 to L-10; A-1 to G-9; A-1 to G-8; or A-1 to E-7 of SEQ ID NO:201 (FIG. 1). Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that these bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Based on the sequence similarity to lipocalin of Bufo marinus, and the prostaglandin D synthase and cpl-1 proteins of Xenopus laevis, translation product of this gene is expected to share at least some biological activities with lipocalin motif-containing proteins, and specifically lipocalin, cpl-1, and prostaglandin D synthase proteins. Such activities are known in the art, some of which are described elsewhere herein.
Specifically, polynucleotides and polypeptides of the invention are also useful for modulating the differentiation of normal and malignant cells, binding to and activating small lipophilic molecules (e.g., retinal, retinoic acid, D/L thyroxine, etc.), modulating the synthesis of prostaglandin D, hormones, etc., and modulating the proliferation and/or dedifferentiation of cancer and neoplastic cells, particularly adenocarcinoma. Polynucleotides and polypeptides of the invention may represent a diagnostic marker for colon adenocarcinoma, and adenocarcinoma in general. The full-length protein should be a secreted protein, based upon homology to the lipocalin family.
Therefore, it is secreted into serum, urine, or feces and thus the levels is assayable from patient samples. Assuming specific expression levels are reflective of the presence of adenocarcinoma, this would provide a convenient diagnostic for early detection. In addition, expression of this gene product may also be linked to the progression of the disease, and therefore may itself actually represent a therapeutic or therapeutic target for the treatment of cancer. Therefore, based upon the tissue distribution of this protein in adenocarcinoma cells and tissues, antagonists directed against this protein is useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene.
Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, lymph, urine, seminal fluid, or feces and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Polynucleotides and polypeptides of the invention may play an important role in the pathogenesis of human cancers and cellular transformation, particularly those of the gastrointestinal, endocrine, and immune systems, and specifically of colon adenocarcinoma, cervical adenocarcinoma, and blood cells. Polynucleotides and polypeptides of the invention may also be involved in the pathogenesis of developmental abnormalities based upon its potential effects on proliferation and differentiation of cells and tissue cell types. Due to the potential proliferating and differentiating activity of said polynucleotides and polypeptides, the invention is useful as a therapeutic agent in inducing tissue regeneration, for treating inflammatory conditions (e.g., inflammatory bowel syndrome, diverticulitis, etc.). Moreover, the invention is useful in modulating the immune response to aberrant polypeptides, as may exist in rapidly proliferating cells and tissue cell types, particularly in adenocarcinoma cells, and other cancers.
This gene is expressed primarily in colon adenocarcinoma, cervical adenocarcinoma, and cell line HeLa S3.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: proliferative diseases and/or disorders, particularly adenocarcinomas. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the gastrointestinal, endocrine, and immune systems, expression of this gene at significantly higher or lower levels is routinely detected in certain tissues or cell types (e.g., gastrointestinal, reproductive, endocrine, immune, and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes shown in SEQ ID NO: 108 as residues: Ser-66 to Ser-72, Pro-104 to Pro-110 (amino acid residues Ser-79 to Ser-85, Pro-117 to 123 of SEQ ID NO:201). Polynucleotides encoding said polypeptides are also encompassed by the invention as are antibodies that bind said epitopes, domains, or other polypeptides of the invention.
The tissue distribution in colon adenocarcinoma indicates polynucleotides and polypeptides corresponding to this gene are useful for the diagnosis and treatment of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cinfectious diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous Disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s Disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. The protein product of this gene is thought to be involved in allergy and Th2 mediated responses. Therefore, antagonists of this protein is useful therapeutically for the treatment, detection, and/or prevention of allergic responses, inhibiting eosinophil and basophil activation and release of mediators, and toxic shock syndromes.
Alternatively, the expression within cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA).
Alternatively, this gene product is involved in the pattern of cellular proliferation that accompanies early embryogenesis. Thus, aberrant expression of this gene product in tissuesxe2x80x94particularly adult tissuesxe2x80x94may correlate with patterns of abnormal cellular proliferation, such as found in various cancers. In addition, other lipocalin family members, specifically cpl1, have been associated with playing a key role in early embryonic development. Through homology, it is expected that polypeptides and polynucleotides of the present invention may also play similar roles. Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus this protein may modulate apoptosis or tissue differentiation and is useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases.
The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:37 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 556 of SEQ ID NO:37, b is an integer of 15 to 570, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:37, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 28
The gene encoding the disclosed cDNA is believed to reside on chromosome 6. Accordingly, polynucleotides related to this invention are useful as a marker in linkage analysis for chromosome 6.
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides) are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
This gene is expressed primarily in osteoclastoma, T-cell, pineal gland, adipose tissue, placenta, dendritic cells, fetal tissue (e.g., heart) and to a lesser extent in many other tissues.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: immune disorders. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., immune, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 109 as residues: Glu-2 to Ser-13, Pro-75 to Leu-80. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in immune cells (e.g., T-cells) indicates the protein product of this clone is useful for the diagnosis and treatment of a variety of immune system disorders. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:38 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 3215 of SEQ ID NO:38, b is an integer of 15 to 3229, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:38, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 29
The polypeptide of this gene has been determined to have a transmembrane domain at about amino acid position 3-19 of the amino acid sequence referenced in Table 1 for this gene. Moreover, a cytoplasmic tail encompassing amino acids 20-75 of this protein has also been determined. Based upon these characteristics, it is believed that the protein product of this gene shares structural features to type Ib membrane proteins.
This gene is expressed primarily in parathyroid tumor, brain, placenta, ovarian cancer, healing groin wound, osteoclastoma and to a lesser extent in many other tissues.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of diseases and conditions which include but are not limited to: ovarian cancer, neurological disorders, and/or parathyroid cancer. Similarly, polypeptides and antibodies directed to these polypeptides are useful in providing immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the female reproductive system, endocrine and exocrine system, expression of this gene at significantly higher or lower levels may be routinely detected in certain tissues or cell types (e.g., ovaries, cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or sample taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue or bodily fluid from an individual not having the disorder.
The tissue distribution in parathyroid tumor and ovarian cancer tissue indicates the protein product of this clone would be useful for the detection, treatment, and/or prevention of various endocrine and reproductive disorders and cancers. Representative uses are described in the xe2x80x9cBiological Activityxe2x80x9d, xe2x80x9cHyperproliferative Disordersxe2x80x9d, and xe2x80x9cBinding Activityxe2x80x9d sections below, in Example 11, 17, 18, 19, 20 and 27, and elsewhere herein. Briefly, the protein can be used for the detection, treatment, and/or prevention of Addison""s disease, Cushing""s Syndrome, and disorders and/or cancers of the pancreas (e.g. diabetes mellitus), adrenal cortex, ovaries, pituitary (e.g., hyper-, hypopituitarism), thyroid (e.g. hyper-, hypothyroidism), parathyroid (e.g. hyper-, hypoparathyroidism), hypothalamus, and testes. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:39 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 497 of SEQ ID NO:39, b is an integer of 15 to 511, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:39, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 30
The translation product of this gene shares sequence homology with apolipoprotein A-IV (see, e.g., Genbank Accession Nos. emb|CAA11020.1|(AJ222966) and gb|AAA35379.1|; all references available through these accessions are hereby incorporated in their entirety by reference herein).
This invention relates to newly identified Apolipoprotein polynucleotides, polypeptides encoded by such polynucleotides, the use of such polynucleotides and polypeptides, as well as the production of such polynucleotides and polypeptides. The polypeptide of the present invention has been putatively identified as a human apolipoprotein A-IV homolog derived from a normal human liver cDNA library, sometimes hereafter referred to as xe2x80x9cApolipoprotein A-IV-Likexe2x80x9d and/or xe2x80x9cApoA-IV-Lxe2x80x9d. The invention also relates to inhibiting the action of such polypeptides.
Apolipoproteins are protein constituents of plasma lipid transport particles. ApoA-IV is associated with triglyceride-rich lipoproteins and HDL, and also occurs in a lipoprotein-free form. It has been proposed to play a role in reverse cholesterol transport on the basis of in vitro properties. It has been demonstrated that apoA-IV can bind to hepatocytes. Since it appears that the expression of our homolog, apoA-IV-L, is liver-enriched, if not liver-specific, perhaps there is some xe2x80x9chand-offxe2x80x9d mechanism, whereby HDL/cholesterol is transported to the liver by apoA-IV and transferred to apoA-IV-L for elimination from the liver. Therefore, apoA-IV-L is intimately involved in cholesterol metabolism, cholesterol transport, and removal of cholesterol from the body. The ApoA-IV protein has also been attributed to regulating food-intake (J Nutr. 1999 Aug;129(8):1503-6).
In transgenic mice that are expressing apoA-IV in the liver, it appears that apoA-IV can protect against atherosclerosis by a mechanism that does not involve an increase in HDL cholesterol concentration. Therefore, perhaps our homolog, apoA-IV-L can also provide protection against atherosclerosis.
Studies have demonstrated that dietary fat clearance is modulated by genetic variation in the apolipoprotein A-IV gene locus. For example, the A-IV-347Ser polymorphism is associated with the variability in low density lipoprotein (LDL)-cholesterol response to dietary therapy. A putative polymorphism has been specifically identified within the present invention (a serine to isoleucine polymorphism at amino acid residue 258 of FIGS. 7A-B (amino acid residue 258 of SEQ ID NO: 212). Perhaps this possible polymorphism, or others as yet undetected in the gene locus for apoA-IV-L may likewise provide a diagnostic for altered lipid/cholesterol/bile metabolism.
Interestingly, other apolipoproteins, specifically apolipoprotein(a) (xe2x80x9capo(a)xe2x80x9d) is a recognized cardiovascular risk factor. Apo(a) is characterized by a high genetic polymorphism with at least 34 isoforms in plasma. Recent studies have shown that in atherothrombosis apo(a) polymorphism could play a role independent of Lp(a) levels. In particular, apo(a) phenotypes seem to have their highest predictive value for coronary heart disease, when apo(a) isoforms are detected by high resolution phenotyping methods and when an adequate operative cut-off of apo(a) polymorphism is used. A strong association between apo(a) phenotypes and coronary heart disease has been also found in hypertensive, diabetic, and uremic patients. Moreover, apo(a) phenotypes seem to correlate well with the severity of coronary atherosclerosis and the age of clinical onset of coronary heart disease. These studies suggest that apo(a) polymorphism may have a great clinical usefulness in a primary prevention setting, since apo(a) phenotypes could be used together with Lp(a) levels as strong genetic predictors of atherothrombosis. The analysis of apo(a) polymorphism appears to be particularly useful in healthy subjects with a family history of atherothrombotic diseases, in patients with diseases at high cardiovascular risk (diabetes, hypertension, hypercholesterolemia) and in subjects with conditions modifying Lp(a) levels (Cardiologia. 1999 Apr;44(4):347-54, and Am J Cardiol. 1999 May 13;83(9B):3F-12F). Thus, it is anticipated that at the present apolipoprotein A-IV-like protein, and/or polymorphisms thereof, may portray similar clinical phenotypes, whose expression levels may also serve as a diagnostic for cardiovascular diseases and/or disorders, if not also for liver diseases and/or disorders.
The polypeptide of the present invention has been putatively identified as a member of the apolipoprotein family and has been termed Apolipoprotein A-IV-Like protein (xe2x80x9cApoA-IV-Lxe2x80x9d). This identification has been made as a result of amino acid sequence homology to the apolipoprotein A-IV of Sus scrofa (emb|CAA11020.1), the human apolipoprotein A-IV (gb|AAA51744.1), and the mouse apolipoprotein A-IV (gb|AAA37214.1).
FIGS. 7A-B show the nucleotide (SEQ ID NO: 40) and deduced amino acid sequence (SEQ ID NO: 212) of ApoA-IV-L. Predicted amino acids from about 1 to about 23 constitute the predicted signal sequence (amino acid residues from about 1 to about 23 in SEQ ID NO: 212) and are represented by the underlined amino acid regions; and nucleic acid residues from about 781 to about 885 (nucleic acid residues from about 781 to about 885 in SEQ ID NO:212 which constitutes the putative polymorphism domain as is represented by the double underlined nucleic acids; and amino acid 258 which constitutes a putative Serine to Isoleucine polymorphism (amino acid residue 258 in SEQ ID NO155 and is represented by the bold amino acid.
FIGS. 8A-8B shows the regions of similarity between the amino acid sequences of the Apolipoprotein A-IV-Like (ApoA-IV-L) protein (SEQ ID NO:212) the apolipoprotein A-IV of Sus scrofa (SEQ ID NO: 206), the human apolipoprotein A-IV (SEQ ID NO: 207), and the mouse apolipoprotein A-IV (SEQ ID NO: 208).
FIG. 9 shows an analysis of the Apolipoprotein A-IV-Like (ApoA-IV-L) amino acid sequence. Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity; amphipathic regions; flexible regions; antigenic index and surface probability are shown.
A polynucleotide encoding a polypeptide of the present invention is obtained from human normal liver, hepatoma, and pancreas tumor tissues. The polynucleotide of this invention was discovered in a human normal liver cDNA library. As shown in FIGS. 7A-B and FIG. 8, ApoA-IV-L has strong conservation between other members of the apolipoprotein A-IV family. The polynucleotide contains an open reading frame encoding the full-length apolipoprotein A-IV polypeptide of 366 amino acids, and a predicted molecular weight of 41.237 kilodaltons. ApoA-IV-L exhibits a high degree of homology at the amino acid level to the apolipoprotein A-IV of Sus scrofa, the human apolipoprotein A-IV, and the mouse apolipoprotein A-IV (as shown in FIG. 8).
The present invention provides isolated nucleic acid molecules comprising a polynucleotide encoding the ApoA-IV-L polypeptide having the amino acid sequence shown in FIGS. 7A-B (SEQ ID NO: 212). The nucleotide sequence shown in FIGS. 7A-B (SEQ ID NO: 40) was obtained by sequencing a cDNA gene (HLDRR08), which was deposited on Sep. 27, 1999 at the American Type Culture Collection, and given Accession Number PTA-796. The deposited gene (HLDRR08) is inserted in the pCMV Sport 3.0 plasmid (Life Technologies, Rockville, Md.) using the SalI/NotI restriction endonuclease cleavage sites.
The present invention is further directed to fragments of the isolated nucleic acid molecules described herein. By a fragment of an isolated DNA molecule having the nucleotide sequence of the deposited cDNA or the nucleotide sequence shown in SEQ ID NO: 40 is intended DNA fragments at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt in length which are useful as diagnostic probes and primers as discussed herein. Of course, larger fragments 50-1500 nt in length are also useful according to the present invention, as are fragments corresponding to most, if not all, of the nucleotide sequence of the deposited cDNA or as shown in SEQ ID NO: 40. By a fragment at least 20 nt in length, for example, is intended fragments which include 20 or more contiguous bases from the nucleotide sequence of the deposited cDNA or the nucleotide sequence as shown in SEQ ID NO: 40. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited size, larger nucleotides, at either terminus or at both termini.
Representative examples of ApoA-IV-L polynucleotide fragments of the invention include, for example, fragments that comprise, or
Alternatively, consist of, a sequence from about nucleotide 1 to about 50, from about 51 to about 100, from about 101 to about 150, from about 151 to about 200, from about 201 to about 250, from about 251 to about 300, from about 301 to about 350, from about 351 to about 400, from about 401 to about 450, from about 451 to about 500, from about 501 to about 550, from about 551 to about 600, from about 601 to about 650, from about 651 to about 700, from about 701 to about 750, from about 751 to about 800, from about 801 to about 850, from about 851 to about 900, from about 901 to about 950, from about 951 to about 1000, from about 1001 to about 1050, from about 1051 to about 1100, from about 1101 to about 1150, from about 1151 to about 1200, from about 1201 to about 1250, from about 1251 to about 1300, from about 1301 to about 1350, from about 1351 to about 1393, from about 64 to about 129, from about 67 to about 1161, and from about 130 to about 1161 of SEQ ID NO: 40 (FIGS. 7A-B), or the complementary strand thereto, or the cDNA contained in the deposited gene. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini.
Alternatively, consisting of, the predicted mature apolipoprotein A-IV-L (amino acid residues from about 24 to about 366 in FIGS. 7A-B (amino acids from about 24 to about 366 in SEQ ID NO: 212); the full-length apolipoprotein A-IV-L (amino acid residues from about 1 to about 366 in FIGS. 7A-B (amino acid residues from about 1 to about 366 in SEQ ID NO: 212); the full-length apolipoprotein A-IV-L minus the start methionine (amino acid residues from about 2 to about 366 in FIGS. 7A-B (amino acid residues from about 2 to about 366 in SEQ ID NO: 212). In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini.
Alternatively, consist of, the putative polymorphic domain, and specifically polynucleotide fragments having a sequence from about nucleotide 825 to about 846, from about 822 to about 849, from about 820 to about 852, from about 817 to about 855, from about 814 to about 858, from about 811 to about 861, from about 808 to about 864, from about 805 to about 867, from about 802 to about 870, from about 799 to about 873, from about 796 to about 876, from about 793 to about 879, from about 790 to about 882, from about 787 to about 885, from about 784 to about 888, and from about 781 to about 891 of SEQ ID NO: 40 (FIGS. 7A-B). In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini, and potentially as many as 10, 20, 30, 40, 50, or 100 nucleotides, at either terminus or at both termini. Such polynucleotide fragments could be used diagnostically to identify individuals, organisms, and/or cells at risk for metabolic, liver, and cardiovascular diseases and/or disorders through the application of such fragments in modern RFLP and SSLP polymorphism analysis. The methodology of such an analysis would readily be apparent to the skilled artisan. Though a few examples are referenced in Methods Mol Biol. 1998;110:1-34, J Clin Lab Anal. 1999;13(5):205-208, and Am. J. Hum. Genet. 44:388-396.
In additional embodiments, the polynucleotides of the invention encode functional attributes of ApoA-IV-L. Preferred embodiments of the invention in this regard include fragments that comprise alpha-helix and alpha-helix forming regions (xe2x80x9calpha-regionsxe2x80x9d), beta-sheet and beta-sheet forming regions (xe2x80x9cbeta-regionsxe2x80x9d), turn and turn-forming regions (xe2x80x9cturn-regionsxe2x80x9d), coil and coil-forming regions (xe2x80x9ccoil-regionsxe2x80x9d), hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions and high antigenic index regions of ApoA-IV-L.
The data representing the structural or functional attributes of ApoA-IV-L set forth in FIG. 9 and/or Table 9, as described above, was generated using the various modules and algorithms of the DNA*STAR set on default parameters. In a preferred embodiment, the data presented in columns VIII, IX, XIII, and XIV of Table 9 can be used to determine regions of ApoA-IV-L which exhibit a high degree of potential for antigenicity. Regions of high antigenicity are determined from the data presented in columns VIII, IX, XIII, and/or XIV by choosing values which represent regions of the polypeptide which are likely to be exposed on the surface of the polypeptide in an environment in which antigen recognition may occur in the process of initiation of an immune response.
Certain preferred regions in these regards are set out in FIG. 9, but may, as shown in Table 9, be represented or identified by using tabular representations of the data presented in FIG. 9. The DNA*STAR computer algorithm used to generate FIG. 9 (set on the original default parameters) was used to present the data in FIG. 9 in a tabular format (See Table 9). The tabular format of the data in FIG. 9 is used to easily determine specific boundaries of a preferred region.
The above-mentioned preferred regions set out in FIG. 9 and in Table 9 include, but are not limited to, regions of the aforementioned types identified by analysis of the amino acid sequence set out in FIGS. 7A-7B. As set out in FIG. 9 and in Table 9, such preferred regions include Garnier-Robson alpha-regions, beta-regions, turn-regions, and coil-regions, Chou-Fasman alpha-regions, beta-regions, and turn-regions, Kyte-Doolittle hydrophilic regions and Hopp-Woods hydrophobic regions, Eisenberg alpha- and beta-amphipathic regions, Karplus-Schulz flexible regions, Jameson-Wolf regions of high antigenic index and Emini surface-forming regions.
Even if deletion of one or more amino acids from the N-terminus of a protein results in modification of loss of one or more biological functions of the protein, other functional activities (e.g., biological activities, ability to multimerize, etc.) may still be retained. For example, the ability of shortened ApoA-IV-L muteins to induce and/or bind to antibodies which recognize the complete or mature forms of the polypeptides generally will be retained when less than the majority of the residues of the complete or mature polypeptide are removed from the N-terminus. Whether a particular polypeptide lacking N-terminal residues of a complete polypeptide retains such immunologic activities can readily be determined by routine methods described herein and otherwise known in the art. It is not unlikely that an ApoA-IV-L mutein with a large number of deleted N-terminal amino acid residues may retain some biological or immunogenic activities. In fact, peptides composed of as few as six ApoA-IV-L amino acid residues may often evoke an immune response.
Accordingly, the present invention further provides polypeptides having one or more residues deleted from the amino terminus of the ApoA-IV-L amino acid sequence shown in FIGS. 7A-7B, up to the serine residue at position number 361 and polynucleotides encoding such polypeptides. In particular, the present invention provides polypeptides comprising the amino acid sequence of residues n1-366 of FIGS. 7A-7B, where n1 is an integer from 2 to 361 corresponding to the position of the amino acid residue in FIGS. 7A-7B (which is identical to the sequence shown as SEQ ID NO: 212).
In another embodiment, N-terminal deletions of the ApoA-IV-L polypeptide can be described by the general formula n2-361, where n2 is a number from 2 to 361, corresponding to the position of amino acid identified in FIGS. 7A-7B. N-terminal deletions of the ApoA-IV-L polypeptide of the invention shown as SEQ ID NO: 212 include polypeptides comprising the amino acid sequence of residues: N-terminal deletions of the ApoA-IV-L polypeptide of the invention shown as SEQ ID NO: 212 include polypeptides comprising, or alternatively consisting of, the amino acid sequence of residues: A-2 to P-366; S-3 to P-366; M-4 to P-366; A-5 to P-366; A-6 to P-366; V-7 to P-366; L-8 to P-366; T-9 to P-366; W-10 to P-366; A-11 to P-366; L-12 to P-366; A-13 to P-366; L-14 to P-366; L-15 to P-366; S-16 to P-366; A-17 to P-366; F-18 to P-366; S-19 to P-366; A-20 to P-366; T-21 to P-366; Q-22 to P-366; A-23 to P-366; R-24 to P-366; K-25 to P-366; G-26 to P-366; F-27 to P-366; W-28 to P-366; D-29 to P-366; Y-30 to P-366; F-31 to P-366; S-32 to P-366; Q-33 to P-366; T-34 to P-366; S-35 to P-366; G-36 to P-366; D-37 to P-366; K-38 to P-366; G-39 to P-366; R-40 to P-366; V-41 to P-366; E-42 to P-366; Q-43 to P-366; I-44 to P-366; H-45 to P-366; Q-46 to P-366; Q-47 to P-366; K-48 to P-366; M-49 to P-366; A-50 to P-366; R-51 to P-366; E-52 to P-366; P-53 to P-366; A-54 to P-366; T-55 to P-366; L-56 to P-366; K-57 to P-366; D-58 to P-366; S-59 to P-366; L-60 to P-366; E-61 to P-366; Q-62 to P-366; D-63 to P-366; L-64 to P-366; N-65 to P-366; N-66 to P-366; M-67 to P-366; N-68 to P-366; K-69 to P-366; F-70 to P-366; L-71 to P-366; E-72 to P-366; K-73 to P-366; L-74 to P-366; R-75 to P-366; P-76 to P-366; L-77 to P-366; S-78 to P-366; G-79 to P-366; S-80 to P-366; E-81 to P-366; A-82 to P-366; P-83 to P-366; R-84 to P-366; L-85 to P-366; P-86 to P-366; Q-87 to P-366; D-88 to P-366; P-89 to P-366; V-90 to P-366; G-91 to P-366; M-92 to P-366; R-93 to P-366; R-94 to P-366; Q-95 to P-366; L-96 to P-366; Q-97 to P-366; E-98 to P-366; E-99 to P-366; L-100 to P-366; E-101 to P-366; E-102 to P-366; V-103 to P-366; K-104 to P-366; A-105 to P-366; R-106 to P-366; L-107 to P-366; Q-108 to P-366; P-109 to P-366; Y-110 to P-366; M-111 to P-366; A-112 to P-366; E-113 to P-366; A-114 to P-366; H-115 to P-366; E-116 to P-366; L-117 to P-366; V-118 to P-366; G-119 to P-366; W-120 to P-366; N-121 to P-366; L-122 to P-366; E-123 to P-366; G-124 to P-366; L-125 to P-366; R-126 to P-366; Q-127 to P-366; Q-128 to P-366; L-129 to P-366; K-130 to P-366; P-131 to P-366; Y-132 to P-366; T-133 to P-366; M-134 to P-366; D-135 to P-366; L-136 to P-366; M-137 to P-366; E-138 to P-366; Q-139 to P-366; V-140 to P-366; A-141 to P-366; L-142 to P-366; R-143 to P-366; V-144 to P-366; Q-145 to P-366; E-146 to P-366; L-147 to P-366; Q-148 to P-366; E-149 to P-366; Q-150 to P-366; L-151 to P-366; R-152 to P-366; V-153 to P-366; V-154 to P-366; G-155 to P-366; E-156 to P-366; D-157 to P-366; T-158 to P-366; K-159 to P-366; A-160 to P-366; Q-161 to P-366; L-162 to P-366; L-163 to P-366; G-164 to P-366; G-165 to P-366; V-166 to P-366; D-167 to P-366; E-168 to P-366; A-169 to P-366; W-170 to P-366; A-171 to P-366; L-172 to P-366; L-173 to P-366; Q-174 to P-366; G-175 to P-366; L-176 to P-366; Q-177 to P-366; S-178 to P-366; R-179 to P-366; V-180 to P-366; V-181 to P-366; H-182 to P-366; H-183 to P-366; T-184 to P-366; G-185 to P-366; R-186 to P-366; F-187 to P-366; K-188 to P-366; E-189 to P-366; L-190 to P-366; F-191 to P-366; H-192 to P-366; P-193 to P-366; Y-194 to P-366; A-195 to P-366; E-196 to P-366; S-197 to P-366; L-198 to P-366; V-199 to P-366; S-200 to P-366; G-201 to P-366; I-202 to P-366; G-203 to P-366; R-204 to P-366; H-205 to P-366; V-206 to P-366; Q-207 to P-366; E-208 to P-366; L-209 to P-366; H-210 to P-366; R-211 to P-366; S-212 to P-366; V-213 to P-366; A-214 to P-366; P-215 to P-366; H-216 to P-366; A-217 to P-366; P-218 to P-366; A-219 to P-366; S-220 to P-366; P-221 to P-366; A-222 to P-366; R-223 to P-366; L-224 to P-366; S-225 to P-366; R-226 to P-366; C-227 to P-366; V-228 to P-366; Q-229 to P-366; V-230 to P-366; L-231 to P-366; S-232 to P-366; R-233 to P-366; K-234 to P-366; L-235 to P-366; T-236 to P-366; L-237 to P-366; K-238 to P-366; A-239 to P-366; K-240 to P-366; A-241 to P-366; L-242 to P-366; H-243 to P-366; A-244 to P-366; R-245 to P-366; I-246 to P-366; Q-247 to P-366; Q-248 to P-366; N-249 to P-366; L-250 to P-366; D-251 to P-366; Q-252 to P-366; L-253 to P-366; R-254 to P-366; E-255 to P-366; E-256 to P-366; L-257 to P-366; I-258 to P-366; R-259 to P-366; A-260 to P-366; F-261 to P-366; A-262 to P-366; G-263 to P-366; T-264 to P-366; G-265 to P-366; T-266 to P-366; E-267 to P-366; E-268 to P-366; G-269 to P-366; A-270 to P-366; G-271 to P-366; P-272 to P-366; D-273 to P-366; P-274 to P-366; Q-275 to P-366; M-276 to P-366; L-277 to P-366; S-278 to P-366; E-279 to P-366; E-280 to P-366; V-281 to P-366; R-282 to P-366; Q-283 to P-366; R-284 to P-366; L-285 to P-366; Q-286 to P-366; A-287 to P-366; F-288 to P-366; R-289 to P-366; Q-290 to P-366; D-291 to P-366; T-292 to P-366; Y-293 to P-366; L-294 to P-366; Q-295 to P-366; I-296 to P-366; A-297 to P-366; A-298 to P-366; F-299 to P-366; T-300 to P-366; R-301 to P-366; A-302 to P-366; I-303 to P-366; D-304 to P-366; Q-305 to P-366; E-306 to P-366; T-307 to P-366; E-308 to P-366; E-309 to P-366; V-310 to P-366; Q-311 to P-366; Q-312 to P-366; Q-313 to P-366; L-314 to P-366; A-315 to P-366; P-316 to P-366; P-317 to P-366; P-318 to P-366; P-319 to P-366; G-320 to P-366; H-321 to P-366; S-322 to P-366; A-323 to P-366; F-324 to P-366; A-325 to P-366; P-326 to P-366; E-327 to P-366; F-328 to P-366; Q-329 to P-366; Q-330 to P-366; T-331 to P-366; D-332 to P-366; S-333 to P-366; G-334 to P-366; K-335 to P-366; V-336 to P-366; L-337 to P-366; S-338 to P-366; K-339 to P-366; L-340 to P-366; Q-341 to P-366; A-342 to P-366; R-343 to P-366; L-344 to P-366; D-345 to P-366; D-346 to P-366; L-347 to P-366; W-348 to P-366; E-349 to P-366; D-350 to P-366; I-351 to P-366; T-352 to P-366; H-353 to P-366; S-354 to P-366; L-355 to P-366; H-356 to P-366; D-357 to P-366; Q-358 to P-366; G-359 to P-366; H-360 to P-366; or S-361 to P-366; of SEQ ID NO: 212. Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that these bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Also as mentioned above, even if deletion of one or more amino acids from the C-terminus of a protein results in modification or loss of one or more biological functions of the protein, other functional activities (e.g., biological activities (e.g., ability to transport lipids, cholesterol transport, metabolize lipoprotein, etc.), ability to multimerize, and the ability to activate lecithin cholesterol actltransferase may still be retained. For example the ability of the shortened ApoA-IV-L mutein to induce and/or bind to antibodies which recognize the complete or mature forms of the polypeptide generally will be retained when less than the majority of the residues of the complete or mature polypeptide are removed from the C-terminus. Whether a particular polypeptide lacking C-terminal residues of a complete polypeptide retains such immunologic activities can readily be determined by routine methods described herein and otherwise known in the art. It is not unlikely that an ApoA-IV-L mutein with a large number of deleted C-terminal amino acid residues may retain some biological or immunogenic activities. In fact, peptides composed of as few as six ApoA-IV-L amino acid residues may often evoke an immune response.
Preferred polypeptides of the invention comprise the following amino acid sequence:
Polynucleotides encoding these polypeptides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that these bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
In another embodiment, the polypeptide sequence illustrated in Table I for this gene (SEQ ID NO:96) represents a potential alternative secreted form of the protein. Based upon the location of the start methionine of this polypeptide sequence with respect to the start methionine of the sequence shown in FIGS. 7A-B (SEQ ID NO: 212), it is unclear which start methionine the cell will utilize during expression. Thus, both SEQ ID NO: 212 and SEQ ID NO:96 are contemplated by the present invention.
Accordingly, the present invention further provides polypeptides having one or more residues deleted from the carboxy terminus of the amino acid sequence of the ApoA-IV-L polypeptide shown in FIGS. 7A-7B, up to the valine residue at position number 7, and polynucleotides encoding such polypeptides. In particular, the present invention provides polypeptides comprising the amino acid sequence of residues 1-m1 of FIGS. 7A-7B, where m1 is an integer from 7 to 336 corresponding to the position of the amino acid residue in FIGS. 7A-7B.
Moreover, the invention provides polynucleotides encoding polypeptides comprising, or alternatively consisting of, the amino acid sequence of C-terminal deletions of the ApoA-IV-L polypeptide of the invention shown as SEQ ID NO: 212 (FIGS. 7A-B) include polypeptides comprising, or alternatively consisting of the amino acid sequence of residues: M-1 to D-365; M-1 to G-364; M-1 to L-363; M-1 to H-362; M-1 to S-361; M-1 to H-360; M-1 to G-359; M-1 to Q-358; M-1 to D-357; M1 to H-356; M-1 to L-355; M-1 to S-354; M-1 to H-353; M-1 to T-352; M-1 to I-351; M-1 to D-350; M-1 to E-349; M-1 to W-348; M-1 to L-347; M-1 to D-346; M-1 to D-345; M-1 to L-344; M-1 to R-343; M-1 to A-342; M-1 to Q-341; M-1 to L-340; M-1 to K-339; M-1 to S-338; M-1 to L-337; M-1 to V-336; M-1 to K-335; M-1 to G-334; M-1 to S-333; M-1 to D-332; M-1 to T-331; M-1 to Q-330; M-1 to Q-329; M-1 to F-328; M-1 to E-327; M-1 to P-326; M-1 to A-325; M-1 to F-324; M-1 to A-323; M-1 to S-322; M-1 to H-321; M-1 to G-320; M-1 to P-319; M-1 to P-318; M-1 to P-317; M-1 to P-316; M-1 to A-315; M-1 to L-314; M-1 to Q-313; M-1 to Q-312; M-1 to Q-311; M-1 to V-310; M-1 to E-309; M-1 to E-308; M-1 to T-307; M-1 to E-306; M-1 to Q-305; M-1 to D-304; M-1 to I-303; M-1 to A-302; M-1 to R-301; M-1 to T-300; M-1 to F-299; M-1 to A-298; M-1 to A-297; M-1 to I-296; M-1 to Q-295; M-1 to L-294; M-1 to Y-293; M-1 to T-292; M-1 to D-291; M-1 to Q-290; M-1 to R-289; M-1 to F-288; M-1 to A-287; M-1 to Q-286; M-1 to L-285; M-1 to R-284; M-1 to Q-283; M-1 to R-282; M-1 to V-281; M-1 to E-280; M-1 to E-279; M-1 to S-278; M-1 to L-277; M-1 to M-276; M-1 to Q-275; M-1 to P-274; M-1 to D-273; M-1 to P-272; M-1 to G-271; M-1 to A-270; M-1 to G-269; M-1 to E-268; M-1 to E-267; M-1 to T-266; M-1 to G-265; M-1 to T-264; M-1 to G-263; M-1 to A-262; M-1 to F-261; M-1 to A-260; M-1 to R-259; M-1 to I-258; M-1 to L-257; M-1 to E-256; M-1 to E-255; M-1 to R-254; M-1 to L-253; M-1 to Q-252; M-1 to D-251; M-1 to L-250; M-1 to N-249; M-1 to Q-248; M-1 to Q-247; M-1 to I-246; M-1 to R-245; M-1 to A-244; M-1 to H-243; M-1 to L-242; M-1 to A-241; M-1 to K-240; M-1 to A-239; M-1 to K-238; M-1 to L-237; M-1 to T-236; M-1 to L-235; M-1 to K-234; M-1 to R-233; M-1 to S-232; M-1 to L-231; M-1 to V-230; M-1 to Q-229; M-1 to V-228; M-1 to C-227; M-1 to R-226; M-1 to S-225; M-1 to L-224; M-1 to R-223; M-1 to A-222; M-1 to P-221; M-1 to S-220; M-1 to A-219; M-1 to P-218; M-1 to A-217; M-1 to H-216; M-1 to P-215; M-1 to A-214; M-1 to V-213; M-1 to S-212; M-1 to R-211; M-1 to H-210; M-1 to L-209; M-1 to E-208; M-1 to Q-207; M-1 to V-206; M-1 to H-205; M-1 to R-204; M-1 to G-203; M-1 to I-202; M-1 to G-201; M-1 to S-200; M-1 to V-199; M-1 to L-198; M-1 to S-197; M-1 to E-196; M-1 to A-195; M-1 to Y-194; M-1 to P-193; M-1 to H-192; M-1 to F-191; M-1 to L-190; M-1 to E-189; M-1 to K-188; M-1 to F-187; M-1 to R-186; M-1 to G-185; M-1 to T-184; M-1 to H-183; M-1 to H-182; M-1 to V-181; M-1 to V-180; M-1 to R-179; M-1 to S-178; M-1 to Q-177; M-1 to L-176; M-1 to G-175; M-1 to Q-174; M-1 to L-173; M-1 to L-172; M-1 to A-171; M-1 to W-170; M-1 to A-169; M-1 to E-168; M-1 to D-167; M-1 to V-166; M-1 to G-165; M-1 to G-164; M-1 to L-163; M-1 to L-162; M-1 to Q-161; M-1 to A-160; M-1 to K-159; M-1 to T-158; M-1 to D-157; M-1 to E-156; M-1 to G-155; M-1 to V-154; M-1 to V-153; M-1 to R-152; M-1 to L-151; M-1 to Q-150; M-1 to E-149; M-1 to Q-148; M-1 to L-147; M-1 to E-146; M-1 to Q-145; M-1 to V-144; M-1 to R-143; M-1 to L-142; M-1 to A-141; M-1 to V-140; M-1 to Q-139; M-1 to E-138; M-1 to M-137; M-1 to L-136; M-1 to D-135; M-1 to M-134; M-1 to T-133; M-1 to Y-132; M-1 to P-131; M-1 to K-130; M-1 to L-129; M-1 to Q-128; M-1 to Q-127; M-1 to R-126; M-1 to L-125; M-1 to G-124; M-1 to E-123; M-1 to L-122; M-1 to N-121; M-1 to W-120; M-1 to G-119; M-1 to V-118; M-1 to L-117; M-1 to E-116; M-1 to H-115; M-1 to A-114; M-1 to E-113; M-1 to A-112; M-1 to M-111; M-1 to Y-110; M-1 to P-109; M-1 to Q-108; M-1 to L-107; M-1 to R-106; M-1 to A-105; M-1 to K-104; M-1 to V-103; M-1 to E-102; M-1 to E-101; M-1 to L-100; M-1 to E-99; M-1 to E-98; M-1 to Q-97; M-1 to L-96; M-1 to Q-95; M-1 to R-94; M-1 to R-93; M-1 to M-92; M-1 to G-91; M-1 to V-90; M-1 to P-89; M-1 to D-88; M-1 to Q-87; M-1 to P-86; M-1 to L-85; M-1 to R-84; M-1 to P-83; M-1 to A-82; M-1 to E-81; M-1 to S-80; M-1 to G-79; M-1 to S-78; M-1 to L-77; M-1 to P-76; M-1 to R-75; M-1 to L-74; M-1 to K-73; M-1 to E-72; M-1 to L-71; M-1 to F-70; M-1 to K-69; M-1 to N-68; M-1 to M-67; M-1 to N-66; M-1 to N-65; M-1 to L-64; M-1 to D-63; M-1 to Q-62; M-1 to E-61; M-1 to L-60; M-1 to S-59; M-1 to D-58; M-1 to K-57; M-1 to L-56; M-1 to T-55; M-1 to A-54; M-1 to P-53; M-1 to E-52; M-1 to R-51; M-1 to A-50; M-1 to M-49; M-1 to K-48; M-1 to Q-47; M-1 to Q-46; M-1 to H-45; M-1 to I-44; M-1 to Q-43; M-1 to E-42; M-1 to V-41; M-1 to R-40; M-1 to G-39; M-1 to K-38; M-1 to D-37; M-1 to G-36; M-1 to S-35; M-1 to T-34; M-1 to Q-33; M-1 to S-32; M-1 to F-31; M-1 to Y-30; M-1 to D-29; M-1 to W-28; M-1 to F-27; M-1 to G-26; M-1 to K-25; M-1 to R-24; M-1 to A-23; M-1 to Q-22; M-1 to T-21; M-1 to A-20; M-1 to S-19; M-1 to F-18; M-1 to A-17; M-1 to S-16; M-1 to L-15; M-1 to L-14; M-1 to A-13; M-1 to L-12; M-1 to A-11; M-1 to W-10; M-1 to T-9; M-1 to L-8; M-1 to V-7; and M-1 to A-6; of SEQ ID NO: 212. Polypeptides encoded by these polynucleotides are also encompassed by the invention.
Moreover, the invention provides polynucleotides encoding polypeptides comprising, or alternatively consisting of, the following amino acid sequences of C-terminal deletions of the mature ApoA-IV-L polypeptide of the invention shown as SEQ ID NO: 212 (FIGS. 7A-B): R-24 to D-365; R-24 to G-364; R-24 to L-363; R-24 to H-362; R-24 to S-361; R-24 to H-360; R-24 to G-359; R-24 to Q-358; R-24 to D-357; R-24 to H-356; R-24 to L-355; R-24 to S-354; R-24 to H-353; R-24 to T-352; R-24 to I-351; R-24 to D-350; R-24 to E-349; R-24 to W-348; R-24 to L-347; R-24 to D-346; R-24 to D-345; R-24 to L-344; R-24 to R-343; R-24 to A-342; R-24 to Q-341; R-24 to L-340; R-24 to K-339; R-24 to S-338; R-24 to L-337; R-24 to V-336; R-24 to K-335; R-24 to G-334; R-24 to S-333; R-24 to D-332; R-24 to T-331; R-24 to Q-330; R-24 to Q-329; R-24 to F-328; R-24 to E-327; R-24 to P-326; R-24 to A-325; R-24 to F-324; R-24 to A-323; R-24 to S-322; R-24 to H-321; R-24 to G-320; R-24 to P-319; R-24 to P-318; R-24 to P-317; R-24 to P-316; R-24 to A-315; R-24 to L-314; R-24 to Q-313; R-24 to Q-312; R-24 to Q-311; R-24 to V-310; R-24 to E-309; R-24 to E-308; R-24 to T-307; R-24 to E-306; R-24 to Q-305; R-24 to D-304; R-24 to I-303; R-24 to A-302; R-24 to R-301; R-24 to T-300; R-24 to F-299; R-24 to A-298; R-24 to A-297; R-24 to I-296; R-24 to Q-295; R-24 to L-294; R-24 to Y-293; R-24 to T-292; R-24 to D-291; R-24 to Q-290; R-24 to R-289; R-24 to F-288; R-24 to A-287; R-24 to Q-286; R-24 to L-285; R-24 to R-284; R-24 to Q-283; R-24 to R-282; R-24 to V-281; R-24 to E-280; R-24 to E-279; R-24 to S-278; R-24 to L-277; R-24 to M-276; R-24 to Q-275; R-24 to P-274; R-24 to D-273; R-24 to P-272; R-24 to G-271; R-24 to A-270; R-24 to G-269; R-24 to E-268; R-24 to E-267; R-24 to T-266; R-24 to G-265; R-24 to T-264; R-24 to G-263; R-24 to A-262; R-24 to F-261; R-24 to A-260; R-24 to R-259; R-24 to I-258; R-24 to L-257; R-24 to E-256; R-24 to E-255; R-24 to R-254; R-24 to L-253; R-24 to Q-252; R-24 to D-251; R-24 to L-250; R-24 to N-249; R-24 to Q-248; R-24 to Q-247; R-24 to I-246; R-24 to R-245; R-24 to A-244; R-24 to H-243; R-24 to L-242; R-24 to A-241; R-24 to K-240; R-24 to A-239; R-24 to K-238; R-24 to L-237; R-24 to T-236; R-24 to L-235; R-24 to K-234; R-24 to R-233; R-24 to S-232; R-24 to L-231; R-24 to V-230; R-24 to Q-229; R-24 to V-228; R-24 to C-227; R-24 to R-226; R-24 to S-225; R-24 to L-224; R-24 to R-223; R-24 to A-222; R-24 to P-221; R-24 to S-220; R-24 to A-219; R-24 to P-218; R-24 to A-217; R-24 to H-216; R-24 to P-215; R-24 to A-214; R-24 to V-213; R-24 to S-212; R-24 to R-211; R-24 to H-210; R-24 to L-209; R-24 to E-208; R-24 to Q-207; R-24 to V-206; R-24 to H-205; R-24 to R-204; R-24 to G-203; R-24 to I-202; R-24 to G-201; R-24 to S-200; R-24 to V-199; R-24 to L-198; R-24 to S-197; R-24 to E-196; R-24 to A-195; R-24 to Y-194; R-24 to P-193; R-24 to H-192; R-24 to F-191; R-24 to L-190; R-24 to E-189; R-24 to K-188; R-24 to F-187; R-24 to R-186; R-24 to G-185; R-24 to T-184; R-24 to H-183; R-24 to H-182; R-24 to V-181; R-24 to V-180; R-24 to R-179; R-24 to S-178; R-24 to Q-177; R-24 to L-176; R-24 to G-175; R-24 to Q-174; R-24 to L-173; R-24 to L-172; R-24 to A-171; R-24 to W-170; R-24 to A-169; R-24 to E-168; R-24 to D-167; R-24 to V-166; R-24 to G-165; R-24 to G-164; R-24 to L-163; R-24 to L-162; R-24 to Q-161; R-24 to A-160; R-24 to K-159; R-24 to T-158; R-24 to D-157; R-24 to E-156; R-24 to G-155; R-24 to V-154; R-24 to V-153; R-24 to R-152; R-24 to L-151; R-24 to Q-150; R-24 to E-149; R-24 to Q-148; R-24 to L-147; R-24 to E-146; R-24 to Q-145; R-24 to V-144; R-24 to R-143; R-24 to L-142; R-24 to A-141; R-24 to V-140; R-24 to Q-139; R-24 to E-138; R-24 to M-137; R-24 to L-136; R-24 to D-135; R-24 to M-134; R-24 to T-133; R-24 to Y-132; R-24 to P-131; R-24 to K-130; R-24 to L-129; R-24 to Q-128; R-24 to Q-127; R-24 to R-126; R-24 to L-125; R-24 to G-124; R-24 to E-123; R-24 to L-122; R-24 to N-121; R-24 to W-120; R-24 to G-119; R-24 to V-118; R-24 to L-117; R-24 to E-116; R-24 to H-115; R-24 to A-114; R-24 to E-113; R-24 to A-112; R-24 to M-111; R-24 to Y-110; R-24 to P-109; R-24 to Q-108; R-24 to L-107; R-24 to R-106; R-24 to A-105; R-24 to K-104; R-24 to V-103; R-24 to E-102; R-24 to E-101; R-24 to L-100; R-24 to E-99; R-24 to E-98; R-24 to Q-97; R-24 to L-96; R-24 to Q-95; R-24 to R-94; R-24 to R-93; R-24 to M-92; R-24 to G-91; R-24 to V-90; R-24 to P-89; R-24 to D-88; R-24 to Q-87; R-24 to P-86; R-24 to L-85; R-24 to R-84; R-24 to P-83; R-24 to A-82; R-24 to E-81; R-24 to S-80; R-24 to G-79; R-24 to S-78; R-24 to L-77; R-24 to P-76; R-24 to R-75; R-24 to L-74; R-24 to K-73; R-24 to E-72; R-24 to L-71; R-24 to F-70; R-24 to K-69; R-24 to N-68; R-24 to M-67; R-24 to N-66; R-24 to N-65; R-24 to L-64; R-24 to D-63; R-24 to Q-62; R-24 to E-61; R-24 to L-60; R-24 to S-59; R-24 to D-58; R-24 to K-57; R-24 to L-56; R-24 to T-55; R-24 to A-54; R-24 to P-53; R-24 to E-52; R-24 to R-51; R-24 A-50; R-24 to M-49; R-24 to K-48; R-24 to Q-47; R-24 to Q-46; R-24 to H-45; R-24 to I-44; R-24 to Q-43; R-24 to E-42; R-24 to V-41; R-24 to R-40; R-24 to G-39; R-24 to K-38; R-24 to D-37; R-24 to G-36; R-24 to S-35; R-24 to T-34; R-24 to Q-33; R-24 to S-32; R-24 to F-31; R-24 to Y-30; of SEQ ID NO: 212. Polypeptides encoded by these polynucleotides are also encompassed by the invention. Moreover, fragments and variants of these polypeptides (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridizes, under stringent conditions, to the polynucleotide encoding these polypeptides, or the complement there of are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding these polypeptides are also encompassed by the invention.
In addition, the invention provides nucleic acid molecules having nucleotide sequences related to extensive portions of SEQ ID NO:19 which have been determined from the following related cDNA genes: HLDOE40R (SEQ ID NO:209), HLDOU12R (SEQ ID NO:210), and HLDBC83RA (SEQ ID NO:211).
Based on the sequence similarity to apolipoprotein A-IV of Sus scrofa, the human apolipoprotein A-IV, and the mouse apolipoprotein A-IV, translation product of this gene is expected to share at least some biological activities with apolipoproteins, and specifically apolipoprotein A-IV proteins. Such activities are known in the art, some of which are described elsewhere herein.
Specifically, polynucleotides and polypeptides of the invention are useful for the treatment, detection, and/or prevention of lipid transport and lipoprotein metabolism disorders. Polynucleotides and polypeptides are proposed to be associated with triglyceride-rich lipoproteins and HDL and may play a role in reverse cholesterol transport (cholesterol transport from tissues back to the liver for elimination). Thus, polynucleotides and polypeptides of the invention are useful for treating, detecting, and/or preventing hypercholesterolemia and related disorders. Polynucleotides and polypeptides of the invention are useful for activating lecithin cholesterol acyltransferase and the promotion of cholesterol efflux from cholesterol-preloaded cells. Polymorphisms in apoA-IV are associated with variability in low density lipoprotein (LDL)-cholesterol response to dietary therapy. Moreover, the levels of such polymorphisms (of the 32 currently known to exist in plasma) also appear to correlate with increased incidence and risk for coronary heart disease. Thus, polynucleotides and polypeptides of the invention are useful for the treatment, detection, and/or prevention of cardiovascular diseases and/or disorders, particularly in the protection against atherogenesis in mice. Polynucleotides and polypeptides of the invention are useful as a satiating factor for controlling appetite and long-term regulation of food intake and body weight (chronic ingestion of a high fat diet blunts apoA-IV response to lipid feeding and may explain why chronic ingestion of a high fat diet predisposes animals and human to obesity).
Polynucleotides and polypeptides of the invention is involved in bile metabolism and is useful in the treatment, detection, and/or prevention of metabolism diseases and/or disorders, particularly for lipid metabolism and lipid emulsification. As inferred above, expression levels and/or polymorphisms in apoA-IV-L may represent diagnostic markers for such conditions as variability in low density lipoprotein (LDL)-cholesterol response to dietary therapy or bile disorders.
Polynucleotides and polypeptides of the invention may represent a diagnostic marker for atherogenesis, atherosclerosis, aberrant cholesterol/LDL/HDL plasma level regulation, obesity, hepatoma, liver diseases and/or disorders, metabolic diseases and/or disorders, obesity, and cardiovascular disease, in general. The full-length protein should be a secreted protein, based upon homology to the apolipoprotein family. Therefore, it is secreted into serum, urine, or feces and thus the levels is assayable from patient samples. Assuming specific expression levels are reflective of the presence of metabolic dysfunction (e.g., aberrant cholesterol/LDL/HDL levels, bile synthesis dysfunction, lipoprotein metabolism dysfunction, etc.), this would provide a convenient diagnostic for early detection. In addition, expression of this gene product may also be linked to the progression of metabolic disease, and therefore may itself actually represent a therapeutic or therapeutic target for the treatment of cancer.
Therefore, based upon the tissue distribution of this protein in liver, hepatoma, and pancreatic cells and tissues, in combination with its homology to apolipoproteins, indicates that this protein represents a novel, central player in lipid transport and metabolism. Therefore, antagonists directed against this protein is useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene.
Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, lymph, urine, seminal fluid, or feces and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein.
Polynucleotides and polypeptides of the invention may play an important role in the pathogenesis of human cancers and cellular transformation, particularly those of the gastrointestinal, endocrine, and metabolic systems, and specifically of hepatoma and pancreatic cancers. Polynucleotides and polypeptides of the invention may also be involved in the pathogenesis of developmental abnormalities based upon its potential effects on proliferation and differentiation of cells and tissue cell types. Due to the potential proliferating and differentiating activity of said polynucleotides and polypeptides, the invention is useful as a therapeutic agent in inducing tissue regeneration, for treating inflammatory conditions (e.g., inflammatory bowel syndrome, diverticulitis, etc.). Moreover, the invention is useful in modulating the immune response to aberrant polypeptides, as may exist in rapidly proliferating cells and tissue cell types, particularly in hepatoma cells, tissues, and other cancers.
The tissue distribution in hepatoma. Liver, and pancreatic cancer indicates polynucleotides and polypeptides corresponding to this gene are useful for the diagnosis and treatment of a variety of metabolic and liver disorders. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d, xe2x80x9cinfectious diseasexe2x80x9d, and xe2x80x9cBinding Activityxe2x80x9d sections below, in Example 11, and 27, and elsewhere herein. Briefly, the protein can be used for the detection, treatment, and/or prevention of hepatoblastoma, jaundice, hepatitis, liver metabolic diseases and conditions that are attributable to the differentiation of hepatocyte progenitor cells.
Alternatively, the expression within cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA).
Alternatively, this gene product is involved in the pattern of cellular proliferation that accompanies early embryogenesis. Thus, aberrant expression of this gene product in tissuesxe2x80x94particularly adult tissuesxe2x80x94may correlate with patterns of abnormal cellular proliferation, such as found in various cancers. In addition, other lipocalin family members, specifically cpl1, have been associated with playing a key role in early embryonic development. Through homology, it is expected that polypeptides and polynucleotides of the present invention may also play similar roles. Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions.
Thus this protein may modulate apoptosis or tissue differentiation and is useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 111 as residues: Gln-19 to Trp-25, Tyr-27 to Arg-37, His-42 to Glu-49, Asp-55 to Asn-65, Glu-78 to Gln-84, Arg-91 to Glu-98, Glu-120 to Tyr-129, Gln-244 to Arg-251, Glu-265 to Gln-272, Ile-300 to Pro-313, Glu-324 to Gly-331. Polynucleotides encoding said polypeptides are also encompassed by the invention.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:40 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1379 of SEQ ID NO:40, b is an integer of 15 to 1393, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:40, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 31
In specific embodiments, polypeptides of the invention comprise, or alternatively consists of, the following amino acid sequence:
Moreover, fragments and variants of this polypeptide (such as, for example, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to these polypeptides and polypeptides encoded by the polynucleotide which hybridize, under stringent conditions, to the polynucleotide encoding this polypeptide are encompassed by the invention. Antibodies that bind polypeptides of the invention are also encompassed by the invention. Polynucleotides encoding this polypeptide are also encompassed by the invention.
The gene encoding the disclosed cDNA is believed to reside on chromosome 14. Accordingly, polynucleotides related to this invention are useful as a marker in linkage analysis for chromosome 14.
It has been discovered that this gene is expressed in normal colon, colon cancer, and ulcerative colitis. This gene is also expressed in normal breast tissue, breast lymph node, breast cancer, bone marrow, thymus, and tonsils.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: gastrointestinal, hematopoietic, immunological, and proliferative diseases and/or disorders, particularly colon cancer, and other cancers. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the gastrointestinal, hematopoietic, and immune systems, expression of this gene at significantly higher or lower levels may be detected in certain tissues or cell types (e.g., bone marrow, gastrointestinal, digestive, immune, breast, cancerous and wounded tissues) or bodily fluids (e.g., lymph, bile, chyme, serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 112 as residues: Asp-73 to Asn-79, Ser-90 to Lys-97, Leu-105 to Ala-111, Tyr-127 to Gln-133, Ser-143 to Lys-148, Ser-156 to Gly-161, Arg-192 to Gly-202, Leu-204 to Ser-209, Lys-229 to Asp-237, Pro-248 to Cys-264, Val-312 to Asp-319, Pro-336 to Thr-342, Lys-362 to Pro-369, Gly-408 to Tyr-417, Ser-422 to Thr-430, Asp-445 to Thr-451. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution in ulcerative colitis and colon cancer tissues indicates that polynucleotides and polypeptides of the invention, as well as antibodies directed to polypeptides of the invention, are useful in the treatment, detection, and/or prevention of gastrointestinal disorders, including inflammatory bowel disorders and proliferative diseases, particularly colon cancer. Furthermore, the expression of this gene in bone marrow, thymus, lymph node, and tonsil tissues suggests that polynucleotides and polypeptides of the invention, as well as antibodies directed to polypeptides of the invention, are useful in the detection, treatment, and/or prevention of hematopoietic and immunological disorders. Moreover, the expression within cellular sources marked by proliferating cells indicates this protein may play a role in the regulation of cellular division, and may show utility in the diagnosis, treatment, and/or prevention of developmental diseases and disorders, including cancer, and other proliferative conditions, including colon and breast cancers. Representative uses are described in the xe2x80x9cHyperproliferative Disordersxe2x80x9d and xe2x80x9cRegenerationxe2x80x9d sections below and elsewhere herein. Briefly, developmental tissues rely on decisions involving cell differentiation and/or apoptosis in pattern formation. Dysregulation of apoptosis can result in inappropriate suppression of cell death, as occurs in the development of some cancers, or in failure to control the extent of cell death, as is believed to occur in acquired immunodeficiency and certain neurodegenerative disorders, such as spinal muscular atrophy (SMA). Alternatively, this gene product may be involved in the pattern of cellular proliferation that accompanies early embryogenesis. Thus, aberrant expression of this gene product in tissuesxe2x80x94particularly adult tissuesxe2x80x94may correlate with patterns of abnormal cellular proliferation, such as found in various cancers. Because of potential roles in proliferation and differentiation, this gene product may have applications in the adult for tissue regeneration and the treatment of cancers. It may also act as a morphogen to control cell and tissue type specification. Therefore, the polynucleotides and polypeptides of the present invention are useful in treating, detecting, and/or preventing said disorders and conditions, in addition to other types of degenerative conditions. Thus this protein may modulate apoptosis or tissue differentiation and would be useful in the detection, treatment, and/or prevention of degenerative or proliferative conditions and diseases. The protein is useful in modulating the immune response to aberrant polypeptides, as may exist in proliferating and cancerous cells and tissues. The protein can also be used to gain new insight into the regulation of cellular growth and proliferation. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, to raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:41 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1637 of SEQ ID NO:41, b is an integer of 15 to 1651, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:41, and where b is greater than or equal to a+14.
Features of Protein Encoded by Gene No: 32
The translation product of this gene shares sequence homology with complement subcomponent C1q chain C precursor (see Genbank accession S14351), which is thought to be important in immune responses.
It has been discovered that this gene is expressed primarily in immune and hemopoietic cells and to a lesser extent in various cancer cells.
Polynucleotides and polypeptides of the invention are useful as reagents for differential identification of the tissue(s) or cell type(s) present in a biological sample and for diagnosis of the following diseases and conditions: disorders of the immune and hemopoietic systems and cancer. Similarly, polypeptides and antibodies directed to those polypeptides are useful to provide immunological probes for differential identification of the tissue(s) or cell type(s). For a number of disorders of the above tissues or cells, particularly of the immune and hemopoietic systems, expression of this gene at significantly higher or lower levels may be detected in certain tissues (e.g., cancerous and wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual having such a disorder, relative to the standard gene expression level, i.e., the expression level in healthy tissue from an individual not having the disorder.
Preferred polypeptides of the present invention comprise, or alternatively consist of, one or more immunogenic epitopes immunogenic epitopes shown in SEQ ID NO: 113 as residues: Arg-25 to Gly-31, Pro-45 to Gly-52. Polynucleotides encoding said polypeptides are also encompassed by the invention.
The tissue distribution and homology to complement subcomponent C1q chain C precursor suggests that the protein product of this clone would be useful for treatment and diagnosis of diseases of the immune and hemopoietic systems and cancers. Representative uses are described in the xe2x80x9cImmune Activityxe2x80x9d and xe2x80x9cInfectious Diseasexe2x80x9d sections below, in Example 11, 13, 14, 16, 18, 19, 20, and 27, and elsewhere herein. Briefly, the expression of this gene product indicates a role in regulating the proliferation; survival; differentiation; and/or activation of hematopoietic cell lineages, including blood stem cells. This gene product is involved in the regulation of cytokine production, antigen presentation, or other processes suggesting a usefulness in the treatment of cancer (e.g. by boosting immune responses). Since the gene is expressed in cells of lymphoid origin, the natural gene product is involved in immune functions. Therefore it is also useful as an agent for immunological disorders including arthritis, asthma, immunodeficiency diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to transplanted organs and tissues, such as host-versus-graft and graft-versus-host diseases, or autoimmunity disorders, such as autoimmune infertility, lens tissue injury, demyelination, systemic lupus erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren""s disease, and scleroderma. Moreover, the protein may represent a secreted factor that influences the differentiation or behavior of other blood cells, or that recruits hematopoietic cells to sites of injury. Thus, this gene product is thought to be useful in the expansion of stem cells and committed progenitors of various blood lineages, and in the differentiation and/or proliferation of various cell types. Based upon the tissue distribution of this protein, antagonists directed against this protein may be useful in blocking the activity of this protein. Accordingly, preferred are antibodies which specifically bind a portion of the translation product of this gene. Also provided is a kit for detecting tumors in which expression of this protein occurs. Such a kit comprises in one embodiment an antibody specific for the translation product of this gene bound to a solid support. Also provided is a method of detecting these tumors in an individual which comprises a step of contacting an antibody specific for the translation product of this gene to a bodily fluid from the individual, preferably serum, and ascertaining whether antibody binds to an antigen found in the bodily fluid. Preferably the antibody is bound to a solid support and the bodily fluid is serum. The above embodiments, as well as other treatments and diagnostic tests (kits and methods), are more particularly described elsewhere herein. Furthermore, the protein may also be used to determine biological activity, raise antibodies, as tissue markers, to isolate cognate ligands or receptors, to identify agents that modulate their interactions, in addition to its use as a nutritional supplement. Protein, as well as, antibodies directed against the protein may show utility as a tumor marker Many polynucleotide sequences, such as EST sequences, are publicly available and accessible through sequence databases. Some of these sequences are related to SEQ ID NO:42 and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention. To list every related sequence would be cumbersome. Accordingly, preferably excluded from the present invention are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 to 1094 of SEQ ID NO:42, b is an integer of 15 to 1108, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:42, and where b is greater than or equal to a+14.
Table 1 summarizes the information corresponding to each xe2x80x9cGene No.xe2x80x9d described above. The nucleotide sequence identified as xe2x80x9cNT SEQ ID NO:Xxe2x80x9d was assembled from partially homologous (xe2x80x9coverlappingxe2x80x9d) sequences obtained from the xe2x80x9ccDNA clone IDxe2x80x9d identified in Table 1 and, in some cases, from additional related DNA clones. The overlapping sequences were assembled into a single contiguous sequence of high redundancy (usually three to five overlapping sequences at each nucleotide position), resulting in a final sequence identified as SEQ ID NO:X.
The cDNA Clone ID was deposited on the date and given the corresponding deposit number listed in xe2x80x9cATCC(copyright) Deposit No:Z and Date.xe2x80x9d Some of the deposits contain multiple different clones corresponding to the same gene. xe2x80x9cVectorxe2x80x9d refers to the type of vector contained in the cDNA Clone ID.
xe2x80x9cTotal NT Seq.xe2x80x9d refers to the total number of nucleotides in the contig identified by xe2x80x9cGene No.xe2x80x9d The deposited clone may contain all or most of these sequences, reflected by the nucleotide position indicated as xe2x80x9c5xe2x80x2 NT of Clone Seq.xe2x80x9d and the xe2x80x9c3xe2x80x2 NT of Clone Seq.xe2x80x9d of SEQ ID NO:X. The nucleotide position of SEQ ID NO:X of the putative start codon (methionine) is identified as xe2x80x9c5xe2x80x2 NT of Start Codon.xe2x80x9d Similarly, the nucleotide position of SEQ ID NO:X of the predicted signal sequence is identified as xe2x80x9c5xe2x80x2 NT of First AA of Signal Pep.xe2x80x9d
The translated amino acid sequence, beginning with the methionine, is identified as xe2x80x9cAA SEQ ID NO:Y,xe2x80x9d although other reading frames can also be easily translated using known molecular biology techniques. The polypeptides produced by these alternative open reading frames are specifically contemplated by the present invention.
The first and last amino acid position of SEQ ID NO:Y of the predicted signal peptide is identified as xe2x80x9cFirst AA of Sig Pepxe2x80x9d and xe2x80x9cLast AA of Sig Pep.xe2x80x9d The predicted first amino acid position of SEQ ID NO:Y of the secreted portion is identified as xe2x80x9cPredicted First AA of Secreted Portion.xe2x80x9d Finally, the amino acid position of SEQ ID NO:Y of the last amino acid in the open reading frame is identified as xe2x80x9cLast AA of ORF.xe2x80x9d
SEQ ID NO:X (where X may be any of the polynucleotide sequences disclosed in the sequence listing) and the translated SEQ ID NO:Y (where Y may be any of the polypeptide sequences disclosed in the sequence listing) are sufficiently accurate and otherwise suitable for a variety of uses well known in the art and described further below. For instance, SEQ ID NO:X is useful for designing nucleic acid hybridization probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the cDNA contained in the deposited clone. These probes will also hybridize to nucleic acid molecules in biological samples, thereby enabling a variety of forensic and diagnostic methods of the invention. Similarly, polypeptides identified from SEQ ID NO:Y may be used, for example, to generate antibodies which bind specifically to proteins containing the polypeptides and the secreted proteins encoded by the cDNA clones identified in Table 1.
Nevertheless, DNA sequences generated by sequencing reactions can contain sequencing errors. The errors exist as misidentified nucleotides, or as insertions or deletions of nucleotides in the generated DNA sequence. The erroneously inserted or deleted nucleotides cause frame shifts in the reading frames of the predicted amino acid sequence. In these cases, the predicted amino acid sequence diverges from the actual amino acid sequence, even though the generated DNA sequence may be greater than 99.9% identical to the actual DNA sequence (for example, one base insertion or deletion in an open reading frame of over 1000 bases).
Accordingly, for those applications requiring precision in the nucleotide sequence or the amino acid sequence, the present invention provides not only the generated nucleotide sequence identified as SEQ ID NO:X and the predicted translated amino acid sequence identified as SEQ ID NO:Y, but also a sample of plasmid DNA containing a human cDNA of the invention deposited with the ATCC(copyright), as set forth in Table 1. The nucleotide sequence of each deposited clone can readily be determined by sequencing the deposited clone in accordance with known methods. The predicted amino acid sequence can then be verified from such deposits. Moreover, the amino acid sequence of the protein encoded by a particular clone can also be directly determined by peptide sequencing or by expressing the protein in a suitable host cell containing the deposited human cDNA, collecting the protein, and determining its sequence.
The present invention also relates to the genes corresponding to SEQ ID NO:X, SEQ ID NO:Y, or the deposited clone. The corresponding gene can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material.
Also provided in the present invention are allelic variants, orthologs, and/or species homologs. Procedures known in the art can be used to obtain full-length genes, allelic variants, splice variants, full-length coding portions, orthologs, and/or species homologs of genes corresponding to SEQ ID NO:X, SEQ ID NO:Y, or a deposited clone, using information from the sequences disclosed herein or the clones deposited with the ATCC(copyright). For example, allelic variants and/or species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source for allelic variants and/or the desired homologue.
Table 2 summarizes the expression profile of polynucleotides corresponding to the clones disclosed in Table 1. The first column provides a unique clone identifier, xe2x80x9cClone IDxe2x80x9d, for a cDNA clone related to each contig sequence disclosed in Table 1. Column 2, xe2x80x9cLibrary Codesxe2x80x9d shows the expression profile of tissue and/or cell line libraries which express the polynucleotides of the invention. Each Library Code in column 2 represents a tissue/cell source identifier code corresponding to the Library Code and Library description provided in Table 4. Expression of these polynucleotides was not observed in the other tissues and/or cell libraries tested. One of skill in the art could routinely use this information to identify tissues which show a predominant expression pattern of the corresponding polynucleotide of the invention or to identify polynucleotides which show predominant and/or specific tissue expression.
Table 3, column 1, provides a nucleotide sequence identifier, xe2x80x9cSEQ ID NO:X,xe2x80x9d that matches a nucleotide SEQ ID NO:X disclosed in Table 1, column 5. Table 3, column 2, provides the chromosomal location, xe2x80x9cCytologic Band or Chromosome,xe2x80x9d of polynucleotides corresponding to SEQ ID NO:X. Chromosomal location was determined by finding exact matches to EST and cDNA sequences contained in the NCBI (National Center for Biotechnology Information) UniGene database. Given a presumptive chromosomal location, disease locus association was determined by comparison with the Morbid Map, derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIM(trademark). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.) 2000. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/). If the putative chromosomal location of the Query overlapped with the chromosomal location of a Morbid Map entry, the OMIM reference identification number of the morbid map entry is provided in Table 3, column 3, labelled xe2x80x9cOMIM ID.xe2x80x9d A key to the OMIM reference identification numbers is provided in Table 5.
Table 4 provides a key to the Library Code disclosed in Table 2. Column 1 provides the Library Code disclosed in Table 2, column 2. Column 2 provides a description of the tissue or cell source from which the corresponding library was derived.
Table 5 provides a key to the OMIM reference identification numbers disclosed in Table 3, column 3. OMIM reference identification numbers (Column 1) were derived from Online Mendelian Inheritance in Man (Online Mendelian inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine, (Bethesda, Md.) 2000. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/). Column 2 provides diseases associated with the cytologic band disclosed in Table 3, column 2, as determined using the Morbid Map database.
The polypeptides of the invention can be prepared in any suitable manner. Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
The polypeptides may be in the form of the secreted protein, including the mature form, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification, such as multiple histidine residues, or an additional sequence for stability during recombinant production.
The polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified. A recombinantly produced version of a polypeptide, including the secreted polypeptide, can be substantially purified using techniques described herein or otherwise known in the art, such as, for example, by the one-step method described in Smith and Johnson, Gene 67:31-40 (1988). Polypeptides of the invention also can be purified from natural, synthetic or recombinant sources using techniques described herein or otherwise known in the art, such as, for example, antibodies of the invention raised against the secreted protein.
The present invention provides a polynucleotide comprising, or alternatively consisting of, the nucleic acid sequence of SEQ ID NO:X, and/or a cDNA contained in ATCC(copyright) deposit Z. The present invention also provides a polypeptide comprising, or alternatively, consisting of, the polypeptide sequence of SEQ ID NO:Y and/or a polypeptide encoded by the cDNA contained in ATCC(copyright) deposit Z. Polynucleotides encoding a polypeptide comprising, or alternatively consisting of the polypeptide sequence of SEQ ID NO:Y and/or a polypeptide sequence encoded by the cDNA contained in ATCC(copyright) deposit Z are also encompassed by the invention.
Signal Sequences and Mature Polypeptides
The present invention also encompasses mature forms of a polypeptide having the amino acid sequence of SEQ ID NO:Y and/or the amino acid sequence encoded by the cDNA in a deposited clone. Polynucleotides encoding the mature forms (such as, for example, the polynucleotide sequence in SEQ ID NO:X and/or the polynucleotide sequence contained in the cDNA of a deposited clone) are also encompassed by the invention. Moreover, fragments or variants of these polypeptides (such as, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to these polypeptides, or polypeptides encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of the polynucleotide encoding these polypeptides) are also encompassed by the invention. In preferred embodiments, these fragments or variants retain one or more functional activities of the full-length or mature form of the polypeptide (e.g., biological activity, antigenicity (i.e., ability to bind polypeptide specific antibodies), immunogenicity (i.e., ability to elicit generation of polypeptide specific antibodies), ability to form heteromeric or homomeric multimers/oligomers, and ability to bind cognate receptors or ligands). Antibodies that bind the polypeptides of the invention, and polynucleotides encoding these polypeptides are also encompassed by the invention.
According to the signal hypothesis, proteins secreted by mammalian cells have a signal or secretary leader sequence which is cleaved from the mature protein once export of the growing protein chain across the rough endoplasmic reticulum has been initiated. Most mammalian cells, and even insect cells, cleave secreted proteins with the same specificity. However, in some cases, cleavage of a secreted protein is not entirely uniform, which results in two or more mature species of the protein. Further, it has long been known that cleavage specificity of a secreted protein is ultimately determined by the primary structure of the complete protein, that is, cleavage specificity is inherent in the amino acid sequence of the polypeptide.
Methods for predicting whether a protein has a signal sequence, as well as the cleavage point for that sequence, are available. For instance, the method of McGeoch, Virus Res. 3:271-286 (1985), uses the information from a short N-terminal charged region and a subsequent uncharged region of the complete (uncleaved) protein. The method of von Heinje, Nucleic Acids Res. 14:4683-4690 (1986) uses the information from the residues surrounding the cleavage site, typically residues xe2x88x9213 to +2, where +1 indicates the amino terminus of the cleaved protein. The accuracy of predicting the cleavage points of known mammalian secretory proteins by each of these methods is in the range of 75-80%. (von Heinje, supra.) However, the two methods do not always produce the same predicted cleavage point(s) for a given protein.
In the present case, the deduced amino acid sequence of the secreted polypeptide was analyzed by a computer program called SignalP (Henrik Nielsen et al., Protein Engineering 10:1-6 (1997)), which predicts the sub-cellular localization of a protein based on the amino acid sequence. As part of this computational prediction of localization, the methods of McGeoch and von Heinje are incorporated. The analysis of the amino acid sequences of the secreted proteins described herein by this program provided the results shown in Table 1.
In specific embodiments, polypeptides of the invention comprise, or alternatively consist of, the predicted mature form of the polypeptide as delineated in columns 14 and 15 of Table 1. Moreover, fragments or variants of these polypeptides (such as, fragments as described herein, polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to these polypeptides, or polypeptides encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of the polynucleotide encoding these polypeptides) are also encompassed by the invention. In preferred embodiments, these fragments or variants retain one or more functional activities of the full-length or mature form of the polypeptide (e.g., biological activity, antigenicity (i.e., ability to bind polypeptide specific antibodies), immunogenicity (i.e., ability to elicit generation of polypeptide specific antibodies), ability to form heteromeric or homomeric multimers/oligomers, and ability to bind cognate receptors or ligands). Antibodies that bind the polypeptides of the invention, and polynucleotides encoding these polypeptides are also encompassed by the invention.
Polynucleotides encoding proteins comprising, or consisting of, the predicted mature form of polypeptides of the invention (e.g., polynucleotides having the sequence of SEQ ID NO: X (Table 1, column 5), the sequence delineated in columns 7 and 8 of Table 1, and a sequence encoding the mature polypeptide delineated in columns 14 and 15 of Table 1 (e.g., the sequence of SEQ ID NO:X encoding the mature polypeptide delineated in columns 14 and 15 of Table 1)) are also encompassed by the invention, as are fragments or variants of these polynucleotides (such as, fragments as described herein, polynucleotides at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to these polynucleotides, and nucleic acids which hybridizes under stringent conditions to the complementary strand of the polynucleotide).
As one of ordinary skill would appreciate, however, polypeptide signal sequence cleavage sites cannot be predicted with absolute certainty. For example, within any given organism cleavage of the signal sequence is often not entirely uniform (resulting in more than one mature polypeptide species). Moreover, signal cleavage sites may also vary from organism to organism (also resulting in multiple species of mature polypeptides). Accordingly, the present invention provides secreted polypeptides having a sequence shown in SEQ ID NO:Y which have an N-terminus beginning within 15 residues of the predicted cleavage point (i.e., having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 more or less contiguous residues of SEQ ID NO:Y at the N-terminus when compared to the predicted mature form of the polypeptide (e.g., the mature polypeptide delineated in columns 14 and 15 of Table 1). These polypeptides, and the polynucleotides encoding such polypeptides, are contemplated by the present invention.
Moreover, the signal sequence identified by the above analysis may not necessarily predict the naturally occurring signal sequence. For example, the naturally occurring signal sequence may be further upstream from the predicted signal sequence. However, it is likely that the predicted signal sequence will be capable of directing the secreted protein to the endoplasmic reticulum. Nonetheless, the present invention provides the mature protein produced by expression of the polynucleotide sequence of SEQ ID NO:X and/or the polynucleotide sequence contained in the cDNA of a deposited clone, in a mammalian cell (e.g., COS cells, as described below). These polypeptides, and the polynucleotides encoding such polypeptides, are contemplated by the present invention.
Mature forms of the polypeptide of the present invention also include polypeptides processed at the carboxyl terminus (C-terminus). For example, post-translational processing within any given cell type or organism can also result in polypeptides with truncated C-termini (as compared to the full-length or secreted polypeptides delineated in columns 12 and 15 or columns 14 and 15, respectively, of Table 1). Therefore, in further specific embodiments, polypeptides of the invention comprise, or alternatively consist of, the mature form of the polypeptide having a C-terminus ending within 15 residues of the predicted carboxyl-terminus (i.e., having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 C-terminal residues less than the mature polypeptide delineated in columns 14 and 15 of Table 1).
Thus, mature forms of polypeptides of the present invention include, but are not limited to, polypeptides with amino-terminal and/or carboxyl-terminal truncations of the polypeptide sequences delineated in Table 1, columns 12 and 15. Accordingly, these polypeptides, polynucleotides encoding such polypeptides, and antibodies binding such polypeptides, are contemplated by the present invention.
Polynucleotide and Polypeptide Variants
The present invention is directed to variants of the polynucleotide sequence disclosed in SEQ ID NO:X, the complementary strand thereto, and/or the cDNA sequence contained in a deposited clone.
The present invention also encompasses variants of the polypeptide sequence disclosed in SEQ ID NO:Y and/or encoded by a deposited clone.
xe2x80x9cVariantxe2x80x9d refers to a polynucleotide or polypeptide differing from the polynucleotide or polypeptide of the present invention, but retaining essential properties thereof. Generally, variants are overall closely similar, and, in many regions, identical to the polynucleotide or polypeptide of the present invention.
The present invention is also directed to nucleic acid molecules which comprise, or alternatively consist of, a nucleotide sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to, for example, the nucleotide coding sequence in SEQ ID NO:X or the complementary strand thereto, the nucleotide coding sequence contained in a deposited cDNA clone or the complementary strand thereto, a nucleotide sequence encoding the polypeptide of SEQ ID NO:Y, a nucleotide sequence encoding the polypeptide encoded by the cDNA contained in a deposited clone, and/or polynucleotide fragments of any of these nucleic acid molecules (e.g., those fragments described herein). Polynucleotides which hybridize to these nucleic acid molecules under stringent hybridization conditions or lower stringency conditions are also encompassed by the invention, as are polypeptides encoded by these polynucleotides.
The present invention is also directed to polypeptides which comprise, or alternatively consist of, an amino acid sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identical to, for example, the polypeptide sequence shown in SEQ ID NO:Y, the polypeptide sequence encoded by the cDNA contained in a deposited clone, and/or polypeptide fragments of any of these polypeptides (e.g., those fragments described herein).
By a nucleic acid having a nucleotide sequence at least, for example, 95% xe2x80x9cidenticalxe2x80x9d to a reference nucleotide sequence of the present invention, it is intended that the nucleotide sequence of the nucleic acid is identical to the reference sequence except that the nucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the polypeptide. In other words, to obtain a nucleic acid having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. The query sequence may be an entire sequence shown in Table 1, the ORF (open reading frame), or any fragment specified as described herein.
As a practical matter, whether any particular nucleic acid molecule or polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence of the presence invention can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245(1990)). In a sequence alignment the query and subject sequences are both DNA sequences. An RNA sequence can be compared by converting U""s to T""s. The result of said global sequence alignment is in percent identity. Preferred parameters used in a FASTDB alignment of DNA sequences to calculate percent identity are: Matrix=Unitary, k-tuple=4, Mismatch Penalty=1, Joining Penalty=30, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap Size Penalty 0.05, Window Size=500 or the length of the subject nucleotide sequence, whichever is shorter.
If the subject sequence is shorter than the query sequence because of 5xe2x80x2 or 3xe2x80x2 deletions, not because of internal deletions, a manual correction must be made to the results. This is because the FASTDB program does not account for 5xe2x80x2 and 3xe2x80x2 truncations of the subject sequence when calculating percent identity. For subject sequences truncated at the 5xe2x80x2 or 3xe2x80x2 ends, relative to the query sequence, the percent identity is corrected by calculating the number of bases of the query sequence that are 5xe2x80x2 and 3xe2x80x2 of the subject sequence, which are not matched/aligned, as a percent of the total bases of the query sequence. Whether a nucleotide is matched/aligned is determined by results of the FASTDB sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This corrected score is what is used for the purposes of the present invention. Only bases outside the 5xe2x80x2 and 3xe2x80x2 bases of the subject sequence, as displayed by the FASTDB alignment, which are not matched/aligned with the query sequence, are calculated for the purposes of manually adjusting the percent identity score.
For example, a 90 base subject sequence is aligned to a 100 base query sequence to determine percent identity. The deletions occur at the 5xe2x80x2 end of the subject sequence and therefore, the FASTDB alignment does not show a matched/alignment of the first 10 bases at 5xe2x80x2 end. The 10 unpaired bases represent 10% of the sequence (number of bases at the 5xe2x80x2 and 3xe2x80x2 ends not matched/total number of bases in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 bases were perfectly matched the final percent identity would be 90%. In another example, a 90 base subject sequence is compared with a 100 base query sequence. This time the deletions are internal deletions so that there are no bases on the 5xe2x80x2 or 3xe2x80x2 of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected. Once again, only bases 5xe2x80x2 and 3xe2x80x2 of the subject sequence which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are to made for the purposes of the present invention.
By a polypeptide having an amino acid sequence at least, for example, 95% xe2x80x9cidenticalxe2x80x9d to a query amino acid sequence of the present invention, it is intended that the amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a query amino acid sequence, up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, (indels) or substituted with another amino acid. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to, for instance, an amino acid sequences shown in Table 1 (SEQ ID NO:Y) or to the amino acid sequence encoded by cDNA contained in a deposited clone can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245(1990)). In a sequence alignment the query and subject sequences are either both nucleotide sequences or both amino acid sequences. The result of said global sequence alignment is in percent identity. Preferred parameters used in a FASTDB amino acid alignment are: Matrix=PAM 0, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, Window Size=sequence length, Gap Penalty=5, Gap Size Penalty=0.05, Window Size=500 or the length of the subject amino acid sequence, whichever is shorter.
If the subject sequence is shorter than the query sequence due to N- or C-terminal deletions, not because of internal deletions, a manual correction must be made to the results. This is because the FASTDB program does not account for N- and C-terminal truncations of the subject sequence when calculating global percent identity. For subject sequences truncated at the N- and C-termini, relative to the query sequence, the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C-terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the FASTDB sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This final percent identity score is what is used for the purposes of the present invention. Only residues to the N- and C-termini of the subject sequence, which are not matched/aligned with the query sequence, are considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C-terminal residues of the subject sequence.
For example, a 90 amino acid residue subject sequence is aligned with a 100 residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence and therefore, the FASTDB alignment does not show a matching/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%. In another example, a 90 residue subject sequence is compared with a 100 residue query sequence. This time the deletions are internal deletions so there are no residues at the N- or C-termini of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected. Once again, only residue positions outside the N- and C-terminal ends of the subject sequence, as displayed in the FASTDB alignment, which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are to made for the purposes of the present invention.
The variants may contain alterations in the coding regions, non-coding regions, or both. Especially preferred are polynucleotide variants containing alterations which produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded polypeptide. Nucleotide variants produced by silent substitutions due to the degeneracy of the genetic code are preferred. Moreover, variants in which 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination are also preferred. Polynucleotide variants can be produced for a variety of reasons, e.g., to optimize codon expression for a particular host (change codons in the human mRNA to those preferred by a bacterial host such as E. coli).
Naturally occurring variants are called xe2x80x9callelic variants,xe2x80x9d and refer to one of several alternate forms of a gene occupying a given locus on a chromosome of an organism. (Genes II, Lewin, B., ed., John Wiley and Sons, New York (1985).) These allelic variants can vary at either the polynucleotide and/or polypeptide level and are included in the present invention. Alternatively, non-naturally occurring variants may be produced by mutagenesis techniques or by direct synthesis.
Using known methods of protein engineering and recombinant DNA technology, variants may be generated to improve or alter the characteristics of the polypeptides of the present invention. For instance, one or more amino acids can be deleted from the N-terminus or C-terminus of the secreted protein without substantial loss of biological function. The authors of Ron et al., J. Biol. Chem. 268: 2984-2988 (1993), reported variant KGF proteins having heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino acid residues. Similarly, Interferon gamma exhibited up to ten times higher activity after deleting 8-10 amino acid residues from the carboxy terminus of this protein. (Dobeli et al., J. Biotechnology 7:199-216 (1988).)
Moreover, ample evidence demonstrates that variants often retain a biological activity similar to that of the naturally occurring protein. For example, Gayle and coworkers (J. Biol. Chem 268:22105-22111 (1993)) conducted extensive mutational analysis of human cytokine IL-1a. They used random mutagenesis to generate over 3,500 individual IL-1a mutants that averaged 2.5 amino acid changes per variant over the entire length of the molecule. Multiple mutations were examined at every possible amino acid position. The investigators found that xe2x80x9c[m]ost of the molecule could be altered with little effect on either [binding or biological activity].xe2x80x9d (See, Abstract.) In fact, only 23 unique amino acid sequences, out of more than 3,500 nucleotide sequences examined, produced a protein that significantly differed in activity from wild-type.
Furthermore, even if deleting one or more amino acids from the N-terminus or C-terminus of a polypeptide results in modification or loss of one or more biological functions, other biological activities may still be retained. For example, the ability of a deletion variant to induce and/or to bind antibodies which recognize the secreted form will likely be retained when less than the majority of the residues of the secreted form are removed from the N-terminus or C-terminus. Whether a particular polypeptide lacking N- or C-terminal residues of a protein retains such immunogenic activities can readily be determined by routine methods described herein and otherwise known in the art.
Thus, the invention further includes polypeptide variants which show substantial biological activity. Such variants include deletions, insertions, inversions, repeats, and substitutions selected according to general rules known in the art so as have little effect on activity. For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie et al., Science 247:1306-1310 (1990), wherein the authors indicate that there are two main strategies for studying the tolerance of an amino acid sequence to change.
The first strategy exploits the tolerance of amino acid substitutions by natural selection during the process of evolution. By comparing amino acid sequences in different species, conserved amino acids can be identified. These conserved amino acids are likely important for protein function. In contrast, the amino acid positions where substitutions have been tolerated by natural selection indicates that these positions are not critical for protein function. Thus, positions tolerating amino acid substitution could be modified while still maintaining biological activity of the protein.
The second strategy uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene to identify regions critical for protein function. For example, site directed mutagenesis or alanine-scanning mutagenesis (introduction of single alanine mutations at every residue in the molecule) can be used. (Cunningham and Wells, Science 244:1081-1085 (1989).) The resulting mutant molecules can then be tested for biological activity.
As the authors state, these two strategies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which amino acid changes are likely to be permissive at certain amino acid positions in the protein. For example, most buried (within the tertiary structure of the protein) amino acid residues require nonpolar side chains, whereas few features of surface side chains are generally conserved. Moreover, tolerated conservative amino acid substitutions involve replacement of the aliphatic or hydrophobic amino acids Ala, Val, Leu and Ile; replacement of the hydroxyl residues Ser and Thr; replacement of the acidic residues Asp and Glu; replacement of the amide residues Asn and Gln, replacement of the basic residues Lys, Arg, and His; replacement of the aromatic residues Phe, Tyr, and Trp, and replacement of the small-sized amino acids Ala, Ser, Thr, Met, and Gly.
Besides conservative amino acid substitution, variants of the present invention include (i) substitutions with one or more of the non-conserved amino acid residues, where the substituted amino acid residues may or may not be one encoded by the genetic code, or (ii) substitution with one or more of amino acid residues having a substituent group, or (iii) fusion of the mature polypeptide with another compound, such as a compound to increase the stability and/or solubility of the polypeptide (for example, polyethylene glycol), or (iv) fusion of the polypeptide with additional amino acids, such as, for example, an IgG Fc fusion region peptide, or leader or secretory sequence, or a sequence facilitating purification or (v) fusion of the polypeptide with another compound, such as albumin (including, but not limited to, recombinant albumin (see, e.g., U.S. Pat. No. 5,876,969, issued Mar. 2, 1999, EP Patent 0 413 622, and U.S. Pat. No. 5,766,883, issued Jun. 16, 1998, herein incorporated by reference in their entirety)). Such variant polypeptides are deemed to be within the scope of those skilled in the art from the teachings herein.
For example, polypeptide variants containing amino acid substitutions of charged amino acids with other charged or neutral amino acids may produce proteins with improved characteristics, such as less aggregation. Aggregation of pharmaceutical formulations both reduces activity and increases clearance due to the aggregate""s immunogenic activity. (Pinckard et al., Clin. Exp. Immunol. 2:331-340 (1967); Robbins et al., Diabetes 36: 838-845 (1987); Cleland et al., Crit. Rev. Therapeutic Drug Carrier Systems 10:307-377 (1993).)
A further embodiment of the invention relates to a polypeptide which comprises the amino acid sequence of the present invention having an amino acid sequence which contains at least one amino acid substitution, but not more than 50 amino acid substitutions, even more preferably, not more than 40 amino acid substitutions, still more preferably, not more than 30 amino acid substitutions, and still even more preferably, not more than 20 amino acid substitutions. Of course, in order of ever-increasing preference, it is highly preferable for a peptide or polypeptide to have an amino acid sequence which comprises the amino acid sequence of the present invention, which contains at least one, but not more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid substitutions. In specific embodiments, the number of additions, substitutions, and/or deletions in the amino acid sequence of the present invention or fragments thereof (e.g., the mature form and/or other fragments described herein), is 1-5, 5-10, 5-25, 5-50, 10-50 or 50-150, conservative amino acid substitutions are preferable.
Polynucleotide and Polypeptide Fragments
The present invention is also directed to polynucleotide fragments of the polynucleotides of the invention.
In the present invention, a xe2x80x9cpolynucleotide fragmentxe2x80x9d refers to a short polynucleotide having a nucleic acid sequence which: is a portion of that contained in a deposited clone, or encoding the polypeptide encoded by the cDNA in a deposited clone; is a portion of that shown in SEQ ID NO:X or the complementary strand thereto, or is a portion of a polynucleotide sequence encoding the polypeptide of SEQ ID NO:Y. The nucleotide fragments of the invention are preferably at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt, at least about 50 nt, at least about 75 nt, or at least about 150 nt in length. A fragment xe2x80x9cat least 20 nt in length,xe2x80x9d for example, is intended to include 20 or more contiguous bases from the cDNA sequence contained in a deposited clone or the nucleotide sequence shown in SEQ ID NO:X. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited value, a value larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini. These nucleotide fragments have uses that include, but are not limited to, as diagnostic probes and primers as discussed herein. Of course, larger fragments (e.g., 50, 150, 500, 600, 2000 nucleotides) are preferred.
Moreover, representative examples of polynucleotide fragments of the invention, include, for example, fragments comprising, or alternatively consisting of, a sequence from about nucleotide number 1-50, 51-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 651-700, 701-750, 751-800, 800-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, or 2001 to the end of SEQ ID NO:X, or the complementary strand thereto, or the cDNA contained in a deposited clone. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges, and ranges larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at both termini. Preferably, these fragments encode a polypeptide which has biological activity. More preferably, these polynucleotides can be used as probes or primers as discussed herein. Polynucleotides which hybridize to these nucleic acid molecules under stringent hybridization conditions or lower stringency conditions are also encompassed by the invention, as are polypeptides encoded by these polynucleotides.
In the present invention, a xe2x80x9cpolypeptide fragmentxe2x80x9d refers to an amino acid sequence which is a portion of that contained in SEQ ID NO:Y or encoded by the cDNA contained in a deposited clone. Protein (polypeptide) fragments may be xe2x80x9cfree-standing,xe2x80x9d or comprised within a larger polypeptide of which the fragment forms a part or region, most preferably as a single continuous region. Representative examples of polypeptide fragments of the invention, include, for example, fragments comprising, or alternatively consisting of, from about amino acid number 1-20, 21-40, 41-60, 61-80, 81-100, 102-120, 121-140, 141-160, or 161 to the end of the coding region. Moreover, polypeptide fragments can be about 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150 amino acids in length. In this context xe2x80x9caboutxe2x80x9d includes the particularly recited ranges or values, and ranges or values larger or smaller by several (5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes. Polynucleotides encoding these polypeptides are also encompassed by the invention.
Preferred polypeptide fragments include the secreted protein as well as the mature form. Further preferred polypeptide fragments include the secreted protein or the mature form having a continuous series of deleted residues from the amino or the carboxy terminus, or both. For example, any number of amino acids, ranging from 1-60, can be deleted from the amino terminus of either the secreted polypeptide or the mature form. Similarly, any number of amino acids, ranging from 1-30, can be deleted from the carboxy terminus of the secreted protein or mature form. Furthermore, any combination of the above amino and carboxy terminus deletions are preferred. Similarly, polynucleotides encoding these polypeptide fragments are also preferred.
Also preferred are polypeptide and polynucleotide fragments characterized by structural or functional domains, such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. Polypeptide fragments of SEQ ID NO:Y falling within conserved domains are specifically contemplated by the present invention. Moreover, polynucleotides encoding these domains are also contemplated.
Other preferred polypeptide fragments are biologically active fragments. Biologically active fragments are those exhibiting activity similar, but not necessarily identical, to an activity of the polypeptide of the present invention. The biological activity of the fragments may include an improved desired activity, or a decreased undesirable activity. Polynucleotides encoding these polypeptide fragments are also encompassed by the invention.
Preferably, the polynucleotide fragments of the invention encode a polypeptide which demonstrates a functional activity. By a polypeptide demonstrating a xe2x80x9cfunctional activityxe2x80x9d is meant, a polypeptide capable of displaying one or more known functional activities associated with a full-length (complete) polypeptide of invention protein. Such functional activities include, but are not limited to, biological activity, antigenicity [ability to bind (or compete with a polypeptide of the invention for binding) to an antibody to the polypeptide of the invention], immunogenicity (ability to generate antibody which binds to a polypeptide of the invention), ability to form multimers with polypeptides of the invention, and ability to bind to a receptor or ligand for a polypeptide of the invention.
The functional activity of polypeptides of the invention, and fragments, variants derivatives, and analogs thereof, can be assayed by various methods.
For example, in one embodiment where one is assaying for the ability to bind or compete with full-length polypeptide of the invention for binding to an antibody of the polypeptide of the invention, various immunoassays known in the art can be used, including but not limited to, competitive and non-competitive assay systems using techniques such as radioimmunoassays, ELISA (enzyme linked immunosorbent assay), xe2x80x9csandwichxe2x80x9d immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
In another embodiment, where a ligand for a polypeptide of the invention identified, or the ability of a polypeptide fragment, variant or derivative of the invention to multimerize is being evaluated, binding can be assayed, e.g., by means well-known in the art, such as, for example, reducing and non-reducing gel chromatography, protein affinity chromatography, and affinity blotting. See generally, Phizicky, E., et al., 1995, Microbiol. Rev. 59:94-123. In another embodiment, physiological correlates of binding of a polypeptide of the invention to its substrates (signal transduction) can be assayed.
In addition, assays described herein (see Examples) and otherwise known in the art may routinely be applied to measure the ability of polypeptides of the invention and fragments, variants derivatives and analogs thereof to elicit related biological activity related to that of the polypeptide of the invention (either in vitro or in vivo). Other methods will be known to the skilled artisan and are within the scope of the invention.
The present invention encompasses polypeptides comprising, or alternatively consisting of, an epitope of the polypeptide having an amino acid sequence of SEQ ID NO:Y, or an epitope of the polypeptide sequence encoded by a polynucleotide sequence contained in ATCC(copyright) deposit No. Z or encoded by a polynucleotide that hybridizes to the complement of the sequence of SEQ ID NO:X or contained in ATCC(copyright) deposit No. Z under stringent hybridization conditions or lower stringency hybridization conditions as defined supra. The present invention further encompasses polynucleotide sequences encoding an epitope of a polypeptide sequence of the invention (such as, for example, the sequence disclosed in SEQ ID NO:X), polynucleotide sequences of the complementary strand of a polynucleotide sequence encoding an epitope of the invention, and polynucleotide sequences which hybridize to the complementary strand under stringent hybridization conditions or lower stringency hybridization conditions defined supra.
The term xe2x80x9cepitopes,xe2x80x9d as used herein, refers to portions of a polypeptide having antigenic or immunogenic activity in an animal, preferably a mammal, and most preferably in a human. In a preferred embodiment, the present invention encompasses a polypeptide comprising an epitope, as well as the polynucleotide encoding this polypeptide. An xe2x80x9cimmunogenic epitope,xe2x80x9d as used herein, is defined as a portion of a protein that elicits an antibody response in an animal, as determined by any method known in the art, for example, by the methods for generating antibodies described infra. (See, for example, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983)). The term xe2x80x9cantigenic epitope,xe2x80x9d as used herein, is defined as a portion of a protein to which an antibody can immunospecifically bind its antigen as determined by any method well known in the art, for example, by the immunoassays described herein. Immunospecific binding excludes non-specific binding but does not necessarily exclude cross-reactivity with other antigens. Antigenic epitopes need not necessarily be immunogenic.
Fragments which function as epitopes may be produced by any conventional means. (See, e.g., Houghten, Proc. Natl. Acad. Sci. USA 82:5131-5135 (1985), further described in U.S. Pat. No. 4,631,211).
In the present invention, antigenic epitopes preferably contain a sequence of at least 4, at least 5, at least 6, at least 7, more preferably at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25, at least 30, at least 40, at least 50, and, most preferably, between about 15 to about 30 amino acids. Preferred polypeptides comprising immunogenic or antigenic epitopes are at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acid residues in length. Additional non-exclusive preferred antigenic epitopes include the antigenic epitopes disclosed herein, as well as portions thereof. Antigenic epitopes are useful, for example, to raise antibodies, including monoclonal antibodies, that specifically bind the epitope. Preferred antigenic epitopes include the antigenic epitopes disclosed herein, as well as any combination of two, three, four, five or more of these antigenic epitopes. Antigenic epitopes can be used as the target molecules in immunoassays. (See, for instance, Wilson et al., Cell 37:767-778 (1984); Sutcliffe et al., Science 219:660-666 (1983)).
Similarly, immunogenic epitopes can be used, for example, to induce antibodies according to methods well known in the art. (See, for instance, Sutcliffe et al., supra; Wilson et al., supra; Chow et al., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle et al., J. Gen. Virol. 66:2347-2354 (1985). Preferred immunogenic epitopes include the immunogenic epitopes disclosed herein, as well as any combination of two, three, four, five or more of these immunogenic epitopes. The polypeptides comprising one or more immunogenic epitopes may be presented for eliciting an antibody response together with a carrier protein, such as an albumin, to an animal system (such as rabbit or mouse), or, if the polypeptide is of sufficient length (at least about 25 amino acids), the polypeptide may be presented without a carrier. However, immunogenic epitopes comprising as few as 8 to 10 amino acids have been shown to be sufficient to raise antibodies capable of binding to, at the very least, linear epitopes in a denatured polypeptide (e.g., in Western blotting).
Epitope-bearing polypeptides of the present invention may be used to induce antibodies according to methods well known in the art including, but not limited to, in vivo immunization, in vitro immunization, and phage display methods. See, e.g., Sutcliffe et al., supra; Wilson et al., supra, and Bittle et al., J. Gen. Virol., 66:2347-2354 (1985). If in vivo immunization is used, animals may be immunized with free peptide; however, anti-peptide antibody titer may be boosted by coupling the peptide to a macromolecular carrier, such as keyhole limpet hemacyanin (KLH) or tetanus toxoid. For instance, peptides containing cysteine residues may be coupled to a carrier using a linker such as maleimidobenzoyl-N-hydroxysuccinimide ester (MBS), while other peptides may be coupled to carriers using a more general linking agent such as glutaraldehyde. Animals such as rabbits, rats and mice are immunized with either free or carrier-coupled peptides, for instance, by intraperitoneal and/or intradermal injection of emulsions containing about 100 xcexcg of peptide or carrier protein and Freund""s adjuvant or any other adjuvant known for stimulating an immune response. Several booster injections may be needed, for instance, at intervals of about two weeks, to provide a useful titer of anti-peptide antibody which can be detected, for example, by ELISA assay using free peptide adsorbed to a solid surface. The titer of anti-peptide antibodies in serum from an immunized animal may be increased by selection of anti-peptide antibodies, for instance, by adsorption to the peptide on a solid support and elution of the selected antibodies according to methods well known in the art.
As one of skill in the art will appreciate, and as discussed above, the polypeptides of the present invention comprising an immunogenic or antigenic epitope can be fused to other polypeptide sequences. For example, the polypeptides of the present invention may be fused with the constant domain of immunoglobulins (IgA, IgE, IgG, IgM), or portions thereof (CH1, CH2, CH3, or any combination thereof and portions thereof), or albumin (including but not limited to recombinant albumin (see, e.g., U.S. Pat. No. 5,876,969, issued Mar. 2, 1999, EP Patent 0 413 622, and U.S. Pat. No. 5,766,883, issued Jun. 16, 1998, herein incorporated by reference in their entirety)), resulting in chimeric polypeptides. Such fusion proteins may facilitate purification and may increase half-life in vivo. This has been shown for chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. See, e.g., EP 394,827; Traunecker et al., Nature, 331:84-86 (1988). Enhanced delivery of an antigen across the epithelial barrier to the immune system has been demonstrated for antigens (e.g., insulin) conjugated to an FcRn binding partner such as IgG or Fc fragments (see, e.g., PCT Publications WO 96/22024 and WO 99/04813). IgG Fusion proteins that have a disulfide-linked dimeric structure due to the IgG portion desulfide bonds have also been found to be more efficient in binding and neutralizing other molecules than monomeric polypeptides or fragments thereof alone. See, e.g., Fountoulakis et al., J. Biochem., 270:3958-3964 (1995). Nucleic acids encoding the above epitopes can also be recombined with a gene of interest as an epitope tag (e.g., the hemagglutinin (xe2x80x9cHAxe2x80x9d) tag or flag tag) to aid in detection and purification of the expressed polypeptide. For example, a system described by Janknecht et al. allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al., 1991, Proc. Natl. Acad. Sci. USA 88:8972-897). In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the open reading frame of the gene is translationally fused to an amino-terminal tag consisting of six histidine residues. The tag serves as a matrix binding domain for the fusion protein. Extracts from cells infected with the recombinant vaccinia virus are loaded onto Ni2+ nitriloacetic acid-agarose column and histidine-tagged proteins can be selectively eluted with imidazole-containing buffers.
Additional fusion proteins of the invention may be generated through the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as xe2x80x9cDNA shufflingxe2x80x9d). DNA shuffling may be employed to modulate the activities of polypeptides of the invention, such methods can be used to generate polypeptides with altered activity, as well as agonists and antagonists of the polypeptides. See, generally, U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; 5,834,252; and 5,837,458, and Patten et al., Curr. Opinion Biotechnol. 8:724-33 (1997); Harayama, Trends Biotechnol. 16(2):76-82 (1998); Hansson, et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo and Blasco, Biotechniques 24(2):308-13 (1998) (each of these patents and publications are hereby incorporated by reference in its entirety). In one embodiment, alteration of polynucleotides corresponding to SEQ ID NO:X and the polypeptides encoded by these polynucleotides may be achieved by DNA shuffling. DNA shuffling involves the assembly of two or more DNA segments by homologous or site-specific recombination to generate variation in the polynucleotide sequence. In another embodiment, polynucleotides of the invention, or the encoded polypeptides, may be altered by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods prior to recombination. In another embodiment, one or more components, motifs, sections, parts, domains, fragments, etc., of a polynucleotide encoding a polypeptide of the invention may be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous molecules.
Antibodies
Further polypeptides of the invention relate to antibodies and T-cell antigen receptors (TCR) which immunospecifically bind a polypeptide, polypeptide fragment, or variant of SEQ ID NO:Y, and/or an epitope, of the present invention (as determined by immunoassays well known in the art for assaying specific antibody-antigen binding). Antibodies of the invention include, but are not limited to, polyclonal, monoclonal, multispecific, human, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(abxe2x80x2) fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the invention), and epitope-binding fragments of any of the above. The term xe2x80x9cantibody,xe2x80x9d as used herein, refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that immunospecifically binds an antigen. The immunoglobulin molecules of the invention can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of immunoglobulin molecule. In preferred embodiments, the immunoglobulin molecules of the invention are IgG1. In other preferred embodiments, the immunoglobulin molecules of the invention are IgG4.
Most preferably the antibodies are human antigen-binding antibody fragments of the present invention and include, but are not limited to, Fab, Fabxe2x80x2 and F(abxe2x80x2)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (sdFv) and fragments comprising either a VL or VH domain. Antigen-binding antibody fragments, including single-chain antibodies, may comprise the variable region(s) alone or in combination with the entirety or a portion of the following: hinge region, CH1, CH2, and CH3 domains. Also included in the invention are antigen-binding fragments also comprising any combination of variable region(s) with a hinge region, CH1, CH2, and CH3 domains. The antibodies of the invention may be from any animal origin including birds and mammals. Preferably, the antibodies are human, murine (e.g., mouse and rat), donkey, ship rabbit, goat, guinea pig, camel, horse, or chicken. As used herein, xe2x80x9chumanxe2x80x9d antibodies include antibodies having the amino acid sequence of a human immunoglobulin and include antibodies isolated from human immunoglobulin libraries or from animals transgenic for one or more human immunoglobulin and that do not express endogenous immunoglobulins, as described infra and, for example in, U.S. Pat. No. 5,939,598 by Kucherlapati et al.
The antibodies of the present invention may be monospecific, bispecific, trispecific or of greater multispecificity. Multispecific antibodies may be specific for different epitopes of a polypeptide of the present invention or may be specific for both a polypeptide of the present invention as well as for a heterologous epitope, such as a heterologous polypeptide or solid support material. See, e.g., PCT publications WO 93/17715; WO 92/08802; WO 91/00360; WO 92/05793; Tutt, et al., J. Immunol. 147:60-69 (1991); U.S. Pat. Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920; 5,601,819; Kostelny et al., J. Immunol. 148:1547-1553 (1992).
Antibodies of the present invention may be described or specified in terms of the epitope(s) or portion(s) of a polypeptide of the present invention which they recognize or specifically bind. The epitope(s) or polypeptide portion(s) may be specified as described herein, e.g., by N-terminal and C-terminal positions, by size in contiguous amino acid residues, or listed in the Tables and Figures. Antibodies which specifically bind any epitope or polypeptide of the present invention may also be excluded. Therefore, the present invention includes antibodies that specifically bind polypeptides of the present invention, and allows for the exclusion of the same.
Antibodies of the present invention may also be described or specified in terms of their cross-reactivity. Antibodies that do not bind any other analog, ortholog, or homolog of a polypeptide of the present invention are included. Antibodies that bind polypeptides with at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, and at least 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In specific embodiments, antibodies of the present invention cross-react with murine, rat and/or rabbit homologs of human proteins and the corresponding epitopes thereof. Antibodies that do not bind polypeptides with less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, and less than 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In a specific embodiment, the above-described cross-reactivity is with respect to any single specific antigenic or immunogenic polypeptide, or combination(s) of 2, 3, 4, 5, or more of the specific antigenic and/or immunogenic polypeptides disclosed herein. Further included in the present invention are antibodies which bind polypeptides encoded by polynucleotides which hybridize to a polynucleotide of the present invention under stringent hybridization conditions (as described herein). Antibodies of the present invention may also be described or specified in terms of their binding affinity to a polypeptide of the invention. Preferred binding affinities include those with a dissociation constant or Kd less than 5xc3x9710xe2x88x922 M, 10xe2x88x922 M, 5xc3x9710xe2x88x923 M, 10xe2x88x923 M, 5xc3x9710xe2x88x924 M, 10xe2x88x924 M, 5xc3x9710xe2x88x925 M, 10xe2x88x925 M, 5xc3x9710xe2x88x926 M, 10xe2x88x926 M, 5xc3x9710xe2x88x927 M, 107 M, 5xc3x9710xe2x88x928 M, 10xe2x88x928 M, 5xc3x9710xe2x88x929 M, 10xe2x88x929 M, 5xc3x9710xe2x88x9210 M, 10xe2x88x9210 M, 5xc3x97xe2x88x9211 M, 10xc3x97xe2x88x9211 M, 5xc3x9710xe2x88x9212 M, 10xe2x88x9212M, 5xc3x9710xe2x88x9213 M, 10xe2x88x9213 M, 5xc3x9710xe2x88x9214 M, 10xe2x88x9214 M, 5xc3x9710xe2x88x9215 M, or 10xe2x88x9215 M.
The invention also provides antibodies that competitively inhibit binding of an antibody to an epitope of the invention as determined by any method known in the art for determining competitive binding, for example, the immunoassays described herein. In preferred embodiments, the antibody competitively inhibits binding to the epitope by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50%.
Antibodies of the present invention may act as agonists or antagonists of the polypeptides of the present invention. For example, the present invention includes antibodies which disrupt the receptor/ligand interactions with the polypeptides of the invention either partially or fully. Preferably, antibodies of the present invention bind an antigenic epitope disclosed herein, or a portion thereof. The invention features both receptor-specific antibodies and ligand-specific antibodies. The invention also features receptor-specific antibodies which do not prevent ligand binding but prevent receptor activation. Receptor activation (i.e., signaling) may be determined by techniques described herein or otherwise known in the art. For example, receptor activation can be determined by detecting the phosphorylation (e.g., tyrosine or serine/threonine) of the receptor or its substrate by immunoprecipitation followed by western blot analysis (for example, as described supra). In specific embodiments, antibodies are provided that inhibit ligand activity or receptor activity by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50% of the activity in absence of the antibody.
The invention also features receptor-specific antibodies which both prevent ligand binding and receptor activation as well as antibodies that recognize the receptor-ligand complex, and, preferably, do not specifically recognize the unbound receptor or the unbound ligand. Likewise, included in the invention are neutralizing antibodies which bind the ligand and prevent binding of the ligand to the receptor, as well as antibodies which bind the ligand, thereby preventing receptor activation, but do not prevent the ligand from binding the receptor. Further included in the invention are antibodies which activate the receptor. These antibodies may act as receptor agonists, i.e., potentiate or activate either all or a subset of the biological activities of the ligand-mediated receptor activation, for example, by inducing dimerization of the receptor. The antibodies may be specified as agonists, antagonists or inverse agonists for biological activities comprising the specific biological activities of the peptides of the invention disclosed herein. The above antibody agonists can be made using methods known in the art. See, e.g., PCT publication WO 96/40281; U.S. Pat. No. 5,811,097; Deng et al., Blood 92(6):1981-1988 (1998); Chen et al., Cancer Res. 58(16):3668-3678 (1998); Harrop et al., J. Immunol. 161(4):1786-1794 (1998); Zhu et al., Cancer Res. 58(15):3209-3214 (1998); Yoon et al., J. Immunol. 160(7):3170-3179 (1998); Prat et al., J. Cell. Sci. 111(Pt2):237-247 (1998); Pitard et al., J. Immunol. Methods 205(2):177-190 (1997); Liautard et al., Cytokine 9(4):233-241 (1997); Carlson et al., J. Biol. Chem. 272(17):11295-11301 (1997); Taryman et al., Neuron 14(4):755-762 (1995); Muller et al., Structure 6(9):1153-1167 (1998); Bartunek et al., Cytokine 8(1):14-20 (1996) (which are all incorporated by reference herein in their entireties).
Antibodies of the present invention may be used, for example, but not limited to, to purify, detect, and target the polypeptides of the present invention, including both in vitro and in vivo diagnostic and therapeutic methods. For example, the antibodies have use in immunoassays for qualitatively and quantitatively measuring levels of the polypeptides of the present invention in biological samples. See, e.g., Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988) (incorporated by reference herein in its entirety).
As discussed in more detail below, the antibodies of the present invention may be used either alone or in combination with other compositions. The antibodies may further be recombinantly fused to a heterologous polypeptide at the N- or C-terminus or chemically conjugated (including covalently and non-covalently conjugations) to polypeptides or other compositions. For example, antibodies of the present invention may be recombinantly fused or conjugated to molecules useful as labels in detection assays and effector molecules such as heterologous polypeptides, drugs, radionuclides, or toxins. See, e.g., PCT publications WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No. 5,314,995; and EP 396,387.
The antibodies of the invention include derivatives that are modified, i.e, by the covalent attachment of any type of molecule to the antibody such that covalent attachment does not prevent the antibody from generating an anti-idiotypic response. For example, but not by way of limitation, the antibody derivatives include antibodies that have been modified, e.g., by glycosylation, acetylation, pegylation, phosphylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. Additionally, the derivative may contain one or more non-classical amino acids.
The antibodies of the present invention may be generated by any suitable method known in the art. Polyclonal antibodies to an antigen-of-interest can be produced by various procedures well known in the art. For example, a polypeptide of the invention can be administered to various host animals including, but not limited to, rabbits, mice, rats, etc. to induce the production of sera containing polyclonal antibodies specific for the antigen. Various adjuvants may be used to increase the immunological response, depending on the host species, and include but are not limited to, Freund""s (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and corynebacterium parvum. Such adjuvants are also well known in the art.
Monoclonal antibodies can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof. For example, monoclonal antibodies can be produced using hybridoma techniques including those known in the art and taught, for example, in Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling, et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563-681 (Elsevier, N.Y., 1981) (said references incorporated by reference in their entireties). The term xe2x80x9cmonoclonal antibodyxe2x80x9d as used herein is not limited to antibodies produced through hybridoma technology. The term xe2x80x9cmonoclonal antibodyxe2x80x9d refers to an antibody that is derived from a single clone, including any eukaryotic, prokaryotic, or phage clone, and not the method by which it is produced.
Methods for producing and screening for specific antibodies using hybridoma technology are routine and well known in the art and are discussed in detail in the Examples (e.g., Example 16). In a non-limiting example, mice can be immunized with a polypeptide of the invention or a cell expressing such peptide. Once an immune response is detected, e.g., antibodies specific for the antigen are detected in the mouse serum, the mouse spleen is harvested and splenocytes isolated. The splenocytes are then fused by well known techniques to any suitable myeloma cells, for example cells from cell line SP20 available from the ATCC(copyright). Hybridomas are selected and cloned by limited dilution. The hybridoma clones are then assayed by methods known in the art for cells that secrete antibodies capable of binding a polypeptide of the invention. Ascites fluid, which generally contains high levels of antibodies, can be generated by immunizing mice with positive hybridoma clones.
Accordingly, the present invention provides methods of generating monoclonal antibodies as well as antibodies produced by the method comprising culturing a hybridoma cell secreting an antibody of the invention wherein, preferably, the hybridoma is generated by fusing splenocytes isolated from a mouse immunized with an antigen of the invention with myeloma cells and then screening the hybridomas resulting from the fusion for hybridoma clones that secrete an antibody able to bind a polypeptide of the invention.
Antibody fragments which recognize specific epitopes may be generated by known techniques. For example, Fab and F(abxe2x80x2)2 fragments of the invention may be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(abxe2x80x2)2 fragments). F(abxe2x80x2)2 fragments contain the variable region, the light chain constant region and the CH1 domain of the heavy chain.
For example, the antibodies of the present invention can also be generated using various phage display methods known in the art. In phage display methods, functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them. In a particular embodiment, such phage can be utilized to display antigen binding domains expressed from a repertoire or combinatorial antibody library (e.g., human or murine). Phage expressing an antigen binding domain that binds the antigen of interest can be selected or identified with antigen, e.g., using labeled antigen or antigen bound or captured to a solid surface or bead. Phage used in these methods are typically filamentous phage including fd and M13 binding domains expressed from phage with Fab, Fv or disulfide stabilized Fv antibody domains recombinantly fused to either the phage gene III or gene VIII protein. Examples of phage display methods that can be used to make the antibodies of the present invention include those disclosed in Brinkman et al., J. Immunol. Methods 182:41-50 (1995); Ames et al., J. Immunol. Methods 184:177-186 (1995); Kettleborough et al., Eur. J. Immunol. 24:952-958 (1994); Persic et al., Gene 187 9-18 (1997); Burton et al., Advances in Immunology 57:191-280 (1994); PCT application No. PCT/GB91/01134; PCT publications WO 90/02809; WO 91/10737; WO 92/01047; WO 92/18619; WO 93/11236; WO 95/15982; WO 95/20401; and U.S. Pat. Nos. 5,698,426; 5,223,409; 5,403,484; 5,580,717; 5,427,908; 5,750,753; 5,821,047; 5,571,698; 5,427,908; 5,516,637; 5,780,225; 5,658,727; 5,733,743 and 5,969,108; each of which is incorporated herein by reference in its entirety.
As described in the above references, after phage selection, the antibody coding regions from the phage can be isolated and used to generate whole antibodies, including human antibodies, or any other desired antigen binding fragment, and expressed in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, e.g., as described in detail below. For example, techniques to recombinantly produce Fab, Fabxe2x80x2 and F(abxe2x80x2)2 fragments can also be employed using methods known in the art such as those disclosed in PCT publication WO 92/22324; Mullinax et al., BioTechniques 12(6):864-869 (1992); and Sawai et al., AJRI34:26-34 (1995); and Better et al., Science 240:1041-1043 (1988) (said references incorporated by reference in their entireties).
Examples of techniques which can be used to produce single-chain Fvs and antibodies include those described in U.S. Pat. Nos. 4,946,778 and 5,258,498; Huston et al., Methods in Enzymology 203:46-88 (1991); Shu et al., PNAS90:7995-7999 (1993); and Skerra et al., Science 240:1038-1040 (1988). For some uses, including in vivo use of antibodies in humans and in vitro detection assays, it may be preferable to use chimeric, humanized, or human antibodies. A chimeric antibody is a molecule in which different portions of the antibody are derived from different animal species, such as antibodies having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region. Methods for producing chimeric antibodies are known in the art. See e.g., Morrison, Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Gillies et al., (1989) J. Immunol. Methods 125:191-202; U.S. Pat. Nos. 5,807,715; 4,816,567; and 4,816397, which are incorporated herein by reference in their entirety. Humanized antibodies are antibody molecules from non-human species antibody that binds the desired antigen having one or more complementarity determining regions (CDRs) from the non-human species and a framework regions from a human immunoglobulin molecule. Often, framework residues in the human framework regions will be substituted with the corresponding residue from the CDR donor antibody to alter, preferably improve, antigen binding. These framework substitutions are identified by methods well known in the art, e.g., by modeling of the interactions of the CDR and framework residues to identify framework residues important for antigen binding and sequence comparison to identify unusual framework residues at particular positions. (See, e.g., Queen et al., U.S. Pat. No. 5,585,089; Riechmann et al., Nature 332:323 (1988), which are incorporated herein by reference in their entireties.) Antibodies can be humanized using a variety of techniques known in the art including, for example, CDR-grafting (EP 239,400; PCT publication WO 91/09967; U.S. Pat. Nos. 5,225,539; 5,530,101; and 5,585,089), veneering or resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology 28(4/5):489-498 (1991); Studnicka et al., Protein Engineering 7(6):805-814 (1994); Roguska. et al., PNAS91:969-973 (1994)), and chain shuffling (U.S. Pat. No. 5,565,332).
Completely human antibodies are particularly desirable for therapeutic treatment of human patients. Human antibodies can be made by a variety of methods known in the art including phage display methods described above using antibody libraries derived from human immunoglobulin sequences. See also, U.S. Pat. Nos. 4,444,887 and 4,716,111; and PCT publications WO 98/46645, WO 98/50433, WO 98/24893, WO 98/16654, WO 96/34096, WO 96/33735, and WO 91/10741; each of which is incorporated herein by reference in its entirety.
Human antibodies can also be produced using transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes. For example, the human heavy and light chain immunoglobulin gene complexes may be introduced randomly or by homologous recombination into mouse embryonic stem cells. Alternatively, the human variable region, constant region, and diversity region may be introduced into mouse embryonic stem cells in addition to the human heavy and light chain genes. The mouse heavy and light chain immunoglobulin genes may be rendered non-functional separately or simultaneously with the introduction of human immunoglobulin loci by homologous recombination. In particular, homozygous deletion of the JH region prevents endogenous antibody production. The modified embryonic stem cells are expanded and microinjected into blastocysts to produce chimeric mice. The chimeric mice are then bred to produce homozygous offspring which express human antibodies. The transgenic mice are immunized in the normal fashion with a selected antigen, e.g., all or a portion of a polypeptide of the invention. Monoclonal antibodies directed against the antigen can be obtained from the immunized, transgenic mice using conventional hybridoma technology. The human immunoglobulin transgenes harbored by the transgenic mice rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation. Thus, using such a technique, it is possible to produce therapeutically useful IgG, IgA, IgM and IgE antibodies. For an overview of this technology for producing human antibodies, see Lonberg and Huszar, Int. Rev. Immunol. 13:65-93 (1995). For a detailed discussion of this technology for producing human antibodies and human monoclonal antibodies and protocols for producing such antibodies, see, e.g., PCT publications WO 98/24893; WO 92/01047; WO 96/34096; WO 96/33735; European Patent No. 0 598 877; U.S. Pat. Nos. 5,413,923; 5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793; 5,916,771; and 5,939,598, which are incorporated by reference herein in their entirety. In addition, companies such as Abgenix, Inc. (Freemont, Calif.) and Genpharm (San Jose, Calif.) can be engaged to provide human antibodies directed against a selected antigen using technology similar to that described above.
Completely human antibodies which recognize a selected epitope can be generated using a technique referred to as xe2x80x9cguided selection.xe2x80x9d In this approach a selected non-human monoclonal antibody, e.g., a mouse antibody, is used to guide the selection of a completely human antibody recognizing the same epitope. (Jespers et al., Bio/technology 12:899-903 (1988)).
Further, antibodies to the polypeptides of the invention can, in turn, be utilized to generate anti-idiotype antibodies that xe2x80x9cmimicxe2x80x9d polypeptides of the invention using techniques well known to those skilled in the art. (See, e.g., Greenspan and Bona, FASEB J. 7(5):437-444; (1989) and Nissinoff, J. Immunol. 147(8):2429-2438 (1991)). For example, antibodies which bind to and competitively inhibit polypeptide multimerization and/or binding of a polypeptide of the invention to a ligand can be used to generate anti-idiotypes that xe2x80x9cmimicxe2x80x9d the polypeptide multimerization and/or binding domain and, as a consequence, bind to and neutralize polypeptide and/or its ligand. Such neutralizing anti-idiotypes or Fab fragments of such anti-idiotypes can be used in therapeutic regimens to neutralize polypeptide ligand. For example, such anti-idiotypic antibodies can be used to bind a polypeptide of the invention and/or to bind its ligands/receptors, and thereby block its biological activity.
Polynucleotides Encoding Antibodies
The invention further provides polynucleotides comprising a nucleotide sequence encoding an antibody of the invention and fragments thereof. The invention also encompasses polynucleotides that hybridize under stringent or lower stringency hybridization conditions, e.g., as defined supra, to polynucleotides that encode an antibody, preferably, that specifically binds to a polypeptide of the invention, preferably, an antibody that binds to a polypeptide having the amino acid sequence of SEQ ID NO:Y.
The polynucleotides may be obtained, and the nucleotide sequence of the polynucleotides determined, by any method known in the art. For example, if the nucleotide sequence of the antibody is known, a polynucleotide encoding the antibody may be assembled from chemically synthesized oligonucleotides (e.g., as described in Kutmeier et al., BioTechniques 17:242 (1994)), which, briefly, involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, annealing and ligating of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR.
Alternatively, a polynucleotide encoding an antibody may be generated from nucleic acid from a suitable source. If a clone containing a nucleic acid encoding a particular antibody is not available, but the sequence of the antibody molecule is known, a nucleic acid encoding the immunoglobulin may be chemically synthesized or obtained from a suitable source (e.g., an antibody cDNA library, or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the antibody, such as hybridoma cells selected to express an antibody of the invention) by PCR amplification using synthetic primers hybridizable to the 3xe2x80x2 and 5xe2x80x2 ends of the sequence or by cloning using an oligonucleotide probe specific for the particular gene sequence to identify, e.g., a cDNA clone from a cDNA library that encodes the antibody. Amplified nucleic acids generated by PCR may then be cloned into replicable cloning vectors using any method well known in the art.
Once the nucleotide sequence and corresponding amino acid sequence of the antibody is determined, the nucleotide sequence of the antibody may be manipulated using methods well known in the art for the manipulation of nucleotide sequences, e.g., recombinant DNA techniques, site directed mutagenesis, PCR, etc. (see, for example, the techniques described in Sambrook et al., 1990, Molecular Cloning, A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. and Ausubel et al., eds., 1998, Current Protocols in Molecular Biology, John Wiley and Sons, NY, which are both incorporated by reference herein in their entireties), to generate antibodies having a different amino acid sequence, for example to create amino acid substitutions, deletions, and/or insertions.
In a specific embodiment, the amino acid sequence of the heavy and/or light chain variable domains may be inspected to identify the sequences of the complementarity determining regions (CDRs) by methods that are well know in the art, e.g., by comparison to known amino acid sequences of other heavy and light chain variable regions to determine the regions of sequence hypervariability. Using routine recombinant DNA techniques, one or more of the CDRs may be inserted within framework regions, e.g., into human framework regions to humanize a non-human antibody, as described supra. The framework regions may be naturally occurring or consensus framework regions, and preferably human framework regions (see, e.g., Chothia et al., J. Mol. Biol. 278: 457-479 (1998) for a listing of human framework regions). Preferably, the polynucleotide generated by the combination of the framework regions and CDRs encodes an antibody that specifically binds a polypeptide of the invention. Preferably, as discussed supra, one or more amino acid substitutions may be made within the framework regions, and, preferably, the amino acid substitutions improve binding of the antibody to its antigen. Additionally, such methods may be used to make amino acid substitutions or deletions of one or more variable region cysteine residues participating in an intrachain disulfide bond to generate antibody molecules lacking one or more intrachain disulfide bonds. Other alterations to the polynucleotide are encompassed by the present invention and within the skill of the art.
In addition, techniques developed for the production of xe2x80x9cchimeric antibodiesxe2x80x9d (Morrison et al., Proc. Natl. Acad. Sci. 81:851-855 (1984); Neuberger et al., Nature 312:604-608 (1984); Takeda et al., Nature 314:452-454 (1985)) by splicing genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. As described supra, a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region, e.g., humanized antibodies.
Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778; Bird, Science 242:423-42 (1988); Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988); and Ward et al., Nature 334:544-54 (1989)) can be adapted to produce single chain antibodies. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide. Techniques for the assembly of functional Fv fragments in E. coli may also be used (Skerra et al., Science 242:1038-1041 (1988)).
Methods of Producing Antibodies
The antibodies of the invention can be produced by any method known in the art for the synthesis of antibodies, in particular, by chemical synthesis or preferably, by recombinant expression techniques.
Recombinant expression of an antibody of the invention, or fragment, derivative or analog thereof, (e.g., a heavy or light chain of an antibody of the invention or a single chain antibody of the invention), requires construction of an expression vector containing a polynucleotide that encodes the antibody. Once a polynucleotide encoding an antibody molecule or a heavy or light chain of an antibody, or portion thereof (preferably containing the heavy or light chain variable domain), of the invention has been obtained, the vector for the production of the antibody molecule may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. The invention, thus, provides replicable vectors comprising a nucleotide sequence encoding an antibody molecule of the invention, or a heavy or light chain thereof, or a heavy or light chain variable domain, operably linked to a promoter. Such vectors may include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., PCT Publication WO 86/05807; PCT Publication WO 89/01036; and U.S. Pat. No. 5,122,464) and the variable domain of the antibody may be cloned into such a vector for expression of the entire heavy or light chain.
The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce an antibody of the invention. Thus, the invention includes host cells containing a polynucleotide encoding an antibody of the invention, or a heavy or light chain thereof, or a single chain antibody of the invention, operably linked to a heterologous promoter. In preferred embodiments for the expression of double-chained antibodies, vectors encoding both the heavy and light chains may be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
A variety of host-expression vector systems may be utilized to express the antibody molecules of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody molecule of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing antibody coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). Preferably, bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule. For example, mammalian cells such as Chinese hamster ovary cells (CHO), in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus is an effective expression system for antibodies (Foecking et al., Gene 45:101 (1986); Cockett et al., Bio/Technology 8:2 (1990)).
In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the antibody molecule being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of an antibody molecule, vectors which direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., EMBO J. 2:1791 (1983)), in which the antibody coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye and Inouye, Nucleic Acids Res. 13:3101-3109 (1985); Van Heeke and Schuster, J. Biol. Chem. 24:5503-5509 (1989)); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to matrix glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.
In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The antibody coding sequence may be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter).
In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, the antibody coding sequence of interest may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts. (e.g., see Logan and Shenk, Proc. Natl. Acad. Sci. USA 81:355-359 (1984)). Specific initiation signals may also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see Bittner et al., Methods in Enzymol. 153:51-544 (1987)).
In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. Such mammalian host cells include but are not limited to CHO, VERY, BHK, Hela, COS, MDCK, 293, 3T3, WI38, and in particular, breast cancer cell lines such as, for example, BT483, Hs578T, HTB2, BT20 and T47D, and normal mammary gland cell line such as, for example, CRL7030 and Hs578Bst.
For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the antibody molecule may be engineered. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells may be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method may advantageously be used to engineer cell lines which express the antibody molecule. Such engineered cell lines may be particularly useful in screening and evaluation of compounds that interact directly or indirectly with the antibody molecule.
A number of selection systems may be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223 (1977)), hypoxanthine-guanine phosphoribosyltransferase (Szybalska and Szybalski, Proc. Natl. Acad. Sci. USA 48:202 (1992)), and adenine phosphoribosyltransferase (Lowy et al., Cell 22:817 (1980)) genes can be employed in tk-, hgprt- or aprt-cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al., Natl. Acad. Sci. USA 77:357 (1980); O""Hare et al., Proc. Natl. Acad. Sci. USA 78:1527 (1981)); gpt, which confers resistance to mycophenolic acid (Mulligan and Berg, Proc. Natl. Acad. Sci. USA 78:2072 (1981)); neo, which confers resistance to the aminoglycoside G-418 Clinical Pharmacy 12:488-505; Wu and Wu, Biotherapy 3:87-95 (1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217 (1993); May, 1993, TIB TECH 11(5):155-215); and hygro, which confers resistance to hygromycin (Santerre et al., Gene 30:147 (1984)). Methods commonly known in the art of recombinant DNA technology may be routinely applied to select the desired recombinant clone, and such methods are described, for example, in Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley and Sons, NY (1993); Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990); and in Chapters 12 and 13, Dracopoli et al. (eds), Current Protocols in Human Genetics, John Wiley and Sons, NY (1994); Colberre-Garapin et al., J. Mol. Biol. 150:1 (1981), which are incorporated by reference herein in their entireties.
The expression levels of an antibody molecule can be increased by vector amplification (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol.3. (Academic Press, New York, 1987)). When a marker in the vector system expressing antibody is amplifiable, increase in the level of inhibitor present in culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody will also increase (Crouse et al., Mol. Cell. Biol. 3:257 (1983)).
The host cell may be co-transfected with two expression vectors of the invention, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide. The two vectors may contain identical selectable markers which enable equal expression of heavy and light chain polypeptides. Alternatively, a single vector may be used which encodes, and is capable of expressing, both heavy and light chain polypeptides. In such situations, the light chain should be placed before the heavy chain to avoid an excess of toxic free heavy chain (Proudfoot, Nature 322:52 (1986); Kohler, Proc. Natl. Acad. Sci. USA 77:2197 (1980)). The coding sequences for the heavy and light chains may comprise cDNA or genomic DNA.
Once an antibody molecule of the invention has been produced by an animal, chemically synthesized, or recombinantly expressed, it may be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. In addition, the antibodies of the present invention or fragments thereof can be fused to heterologous polypeptide sequences described herein or otherwise known in the art, to facilitate purification.
The present invention encompasses antibodies recombinantly fused or chemically conjugated (including both covalently and non-covalently conjugations) to a polypeptide (or portion thereof, preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids of the polypeptide) of the present invention to generate fusion proteins. The fusion does not necessarily need to be direct, but may occur through linker sequences. The antibodies may be specific for antigens other than polypeptides (or portion thereof, preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids of the polypeptide) of the present invention. For example, antibodies may be used to target the polypeptides of the present invention to particular cell types, either in vitro or in vivo, by fusing or conjugating the polypeptides of the present invention to antibodies specific for particular cell surface receptors. Antibodies fused or conjugated to the polypeptides of the present invention may also be used in in vitro immunoassays and purification methods using methods known in the art. See e.g., Harbor et al., supra, and PCT publication WO 93/21232; EP 439,095; Naramura et al., Immunol. Lett. 39:91-99 (1994); U.S. Pat. No. 5,474,981; Gillies et al., PNAS 89:1428-1432 (1992); Fell et al., J. Immunol. 146:2446-2452(1991), which are incorporated by reference in their entireties.
The present invention further includes compositions comprising the polypeptides of the present invention fused or conjugated to antibody domains other than the variable regions. For example, the polypeptides of the present invention may be fused or conjugated to an antibody Fc region, or portion thereof. The antibody portion fused to a polypeptide of the present invention may comprise the constant region, hinge region, CH1 domain, CH2 domain, and CH3 domain or any combination of whole domains or portions thereof. The polypeptides may also be fused or conjugated to the above antibody portions to form multimers. For example, Fc portions fused to the polypeptides of the present invention can form dimers through disulfide bonding between the Fc portions. Higher multimeric forms can be made by fusing the polypeptides to portions of IgA and IgM. Methods for fusing or conjugating the polypeptides of the present invention to antibody portions are known in the art. See, e.g., U.S. Pat. Nos. 5,336,603; 5,622,929; 5,359,046; 5,349,053; 5,447,851; 5,112,946; EP 307,434; EP 367,166; PCT publications WO 96/04388; WO 91/06570; Ashkenazi et al., Proc. Natl. Acad. Sci. USA 88:10535-10539 (1991); Zheng et al., J. Immunol. 154:5590-5600 (1995); and Vil et al., Proc. Natl. Acad. Sci. USA 89:11337-11341(1992) (said references incorporated by reference in their entireties).
As discussed, supra, the polypeptides corresponding to a polypeptide, polypeptide fragment, or a variant of SEQ ID NO:Y may be fused or conjugated to the above antibody portions to increase the in vivo half life of the polypeptides or for use in immunoassays using methods known in the art. Further, the polypeptides corresponding to SEQ ID NO:Y may be fused or conjugated to the above antibody portions to facilitate purification. One reported example describes chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. (EP 394,827; Traunecker et al., Nature 331:84-86 (1988). The polypeptides of the present invention fused or conjugated to an antibody having disulfide-linked dimeric structures (due to the IgG) may also be more efficient in binding and neutralizing other molecules, than the monomeric secreted protein or protein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964 (1995)). In many cases, the Fc part in a fusion protein is beneficial in therapy and diagnosis, and thus can result in, for example, improved pharmacokinetic properties. (EP A 232,262). Alternatively, deleting the Fc part after the fusion protein has been expressed, detected, and purified, would be desired. For example, the Fc portion may hinder therapy and diagnosis if the fusion protein is used as an antigen for immunizations. In drug discovery, for example, human proteins, such as hIL-5, have been fused with Fc portions for the purpose of high-throughput screening assays to identify antagonists of hIL-5. (See, Bennett et al., J. Molecular Recognition 8:52-58 (1995); Johanson et al., J. Biol. Chem. 270:9459-9471 (1995).
Moreover, the antibodies or fragments thereof of the present invention can be fused to marker sequences, such as a peptide to facilitate purification. In preferred embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance, hexa-histidine provides for convenient purification of the fusion protein. Other peptide tags useful for purification include, but are not limited to, the xe2x80x9cHAxe2x80x9d tag, which corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson et al., Cell 37:767 (1984)) and the xe2x80x9cflagxe2x80x9d tag.
The present invention further encompasses antibodies or fragments thereof conjugated to a diagnostic or therapeutic agent. The antibodies can be used diagnostically to, for example, monitor the development or progression of a tumor as part of a clinical testing procedure to, e.g., determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals using various positron emission tomographies, and nonradioactive paramagnetic metal ions. The detectable substance may be coupled or conjugated either directly to the antibody (or fragment thereof) or indirectly, through an intermediate (such as, for example, a linker known in the art) using techniques known in the art. See, for example, U.S. Pat. No. 4,741,900 for metal ions which can be conjugated to antibodies for use as diagnostics according to the present invention. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include 125I, 131I, 111In or 99Tc.
Further, an antibody or fragment thereof may be conjugated to a therapeutic moiety such as a cytotoxin, e.g., a cytostatic or cytocidal agent, a therapeutic agent or a radioactive metal ion, e.g., alpha-emitters such as, for example, 213Bi. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include paclitaxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and vinblastine).
The conjugates of the invention can be used for modifying a given biological response, the therapeutic agent or drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, a-interferon, xcex2-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator, an apoptotic agent, e.g., TNF-alpha, TNF-beta, AIM I (See, International Publication No. WO 97/33899), AIM II (See, International Publication No. WO 97/34911), Fas Ligand (Takahashi et al, Int. Immunol., 6:1567-1574 (1994)), VEGI (See, International Publication No. WO 99/23105), a thrombotic agent or an anti-angiogenic agent, e.g., angiostatin or endostatin; or, biological response modifiers such as, for example, lymphokines, interleukin-1(xe2x80x9cIL-1xe2x80x9d), interleukin-2 (xe2x80x9cIL-2xe2x80x9d), interleukin-6 (xe2x80x9cIL-6xe2x80x9d), granulocyte macrophage colony stimulating factor (xe2x80x9cGM-CSFxe2x80x9d), granulocyte colony stimulating factor (xe2x80x9cG-CSFxe2x80x9d), or other growth factors.
Antibodies may also be attached to solid supports, which are particularly useful for immunoassays or purification of the target antigen. Such solid supports include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene.
Techniques for conjugating such therapeutic moiety to antibodies are well known, see, e.g., Arnon et al., xe2x80x9cMonoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapyxe2x80x9d, in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., xe2x80x9cAntibodies For Drug Deliveryxe2x80x9d, in Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe, xe2x80x9cAntibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Reviewxe2x80x9d, in Monoclonal Antibodies ""84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); xe2x80x9cAnalysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapyxe2x80x9d, in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp. 303-16 (Academic Press 1985), and Thorpe et al., xe2x80x9cThe Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugatesxe2x80x9d, Immunol. Rev. 62:119-58 (1982).
Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Pat. No. 4,676,980, which is incorporated herein by reference in its entirety.
An antibody, with or without a therapeutic moiety conjugated to it, administered alone or in combination with cytotoxic factor(s) and/or cytokine(s) can be used as a therapeutic.
Immunophenotyping
The antibodies of the invention may be utilized for immunophenotyping of cell lines and biological samples. The translation product of the gene of the present invention may be useful as a cell specific marker, or more specifically as a cellular marker that is differentially expressed at various stages of differentiation and/or maturation of particular cell types. Monoclonal antibodies directed against a specific epitope, or combination of epitopes, will allow for the screening of cellular populations expressing the marker. Various techniques can be utilized using monoclonal antibodies to screen for cellular populations expressing the marker(s), and include magnetic separation using antibody-coated magnetic beads, xe2x80x9cpanningxe2x80x9d with antibody attached to a solid matrix (i.e., plate), and flow cytometry (See, e.g., U.S. Pat. No. 5,985,660; and Morrison et al., Cell, 96:737-49 (1999)).
These techniques allow for the screening of particular populations of cells, such as might be found with hematological malignancies (i.e. minimal residual disease (MRD) in acute leukemic patients) and xe2x80x9cnon-selfxe2x80x9d cells in transplantations to prevent Graft-versus-Host Disease (GVHD). Alternatively, these techniques allow for the screening of hematopoietic stem and progenitor cells capable of undergoing proliferation and/or differentiation, as might be found in human umbilical cord blood.
Assays for Antibody Binding
The antibodies of the invention may be assayed for immunospecific binding by any method known in the art. The immunoassays which can be used include but are not limited to competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), xe2x80x9csandwichxe2x80x9d immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to name but a few. Such assays are routine and well known in the art (see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley and Sons, Inc., New York, which is incorporated by reference herein in its entirety). Exemplary immunoassays are described briefly below (but are not intended by way of limitation).
Immunoprecipitation protocols generally comprise lysing a population of cells in a lysis buffer such as RIPA buffer (1% NP-40 or Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 0.15 M NaCl, 0.01 M sodium phosphate at pH 7.2, 1% Trasylol) supplemented with protein phosphatase and/or protease inhibitors (e.g., EDTA, PMSF, aprotinin, sodium vanadate), adding the antibody of interest to the cell lysate, incubating for a period of time (e.g., 1-4 hours) at 4xc2x0 C., adding protein A and/or protein G sepharose beads to the cell lysate, incubating for about an hour or more at 4xc2x0 C., washing the beads in lysis buffer and resuspending the beads in SDS/sample buffer. The ability of the antibody of interest to immunoprecipitate a particular antigen can be assessed by, e.g., western blot analysis. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the binding of the antibody to an antigen and decrease the background (e.g., pre-clearing the cell lysate with sepharose beads). For further discussion regarding immunoprecipitation protocols see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley and Sons, Inc., New York at 10.16.1.
Western blot analysis generally comprises preparing protein samples, electrophoresis of the protein samples in a polyacrylamide gel (e.g., 8%-20% SDS-PAGE depending on the molecular weight of the antigen), transferring the protein sample from the polyacrylamide gel to a membrane such as nitrocellulose, PVDF or nylon, blocking the membrane in blocking solution (e.g., PBS with 3% BSA or non-fat milk), washing the membrane in washing buffer (e.g., PBS-Tween 20), blocking the membrane with primary antibody (the antibody of interest) diluted in blocking buffer, washing the membrane in washing buffer, blocking the membrane with a secondary antibody (which recognizes the primary antibody, e.g., an anti-human antibody) conjugated to an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) or radioactive molecule (e.g., 32P or 125I) diluted in blocking buffer, washing the membrane in wash buffer, and detecting the presence of the antigen. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected and to reduce the background noise. For further discussion regarding western blot protocols see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley and Sons, Inc., New York at 10.8.1.
ELISAs comprise preparing antigen, coating the well of a 96 well microtiter plate with the antigen, adding the antibody of interest conjugated to a detectable compound such as an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) to the well and incubating for a period of time, and detecting the presence of the antigen. In ELISAs the antibody of interest does not have to be conjugated to a detectable compound; instead, a second antibody (which recognizes the antibody of interest) conjugated to a detectable compound may be added to the well. Further, instead of coating the well with the antigen, the antibody may be coated to the well. In this case, a second antibody conjugated to a detectable compound may be added following the addition of the antigen of interest to the coated well. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected as well as other variations of ELISAs known in the art. For further discussion regarding ELISAs see, e.g., Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley and Sons, Inc., New York at 11.2.1.
The binding affinity of an antibody to an antigen and the off-rate of an antibody-antigen interaction can be determined by competitive binding assays. One example of a competitive binding assay is a radioimmunoassay comprising the incubation of labeled antigen (e.g., 3H or 125I) with the antibody of interest in the presence of increasing amounts of unlabeled antigen, and the detection of the antibody bound to the labeled antigen. The affinity of the antibody of interest for a particular antigen and the binding off-rates can be determined from the data by scatchard plot analysis. Competition with a second antibody can also be determined using radioimmunoassays. In this case, the antigen is incubated with antibody of interest conjugated to a labeled compound (e.g., 3H or 125I) in the presence of increasing amounts of an unlabeled second antibody.
Therapeutic Uses
The present invention is further directed to antibody-based therapies which involve administering antibodies of the invention to an animal, preferably a mammal, and most preferably a human, patient for treating one or more of the disclosed diseases, disorders, or conditions. Therapeutic compounds of the invention include, but are not limited to, antibodies of the invention (including fragments, analogs and derivatives thereof as described herein) and nucleic acids encoding antibodies of the invention (including fragments, analogs and derivatives thereof and anti-idiotypic antibodies as described herein). The antibodies of the invention can be used to treat, inhibit or prevent diseases, disorders or conditions associated with aberrant expression and/or activity of a polypeptide of the invention, including, but not limited to, any one or more of the diseases, disorders, or conditions described herein. The treatment and/or prevention of diseases, disorders, or conditions associated with aberrant expression and/or activity of a polypeptide of the invention includes, but is not limited to, alleviating symptoms associated with those diseases, disorders or conditions. Antibodies of the invention may be provided in pharmaceutically acceptable compositions as known in the art or as described herein.
A summary of the ways in which the antibodies of the present invention may be used therapeutically includes binding polynucleotides or polypeptides of the present invention locally or systemically in the body or by direct cytotoxicity of the antibody, e.g. as mediated by complement (CDC) or by effector cells (ADCC). Some of these approaches are described in more detail below. Armed with the teachings provided herein, one of ordinary skill in the art will know how to use the antibodies of the present invention for diagnostic, monitoring or therapeutic purposes without undue experimentation.
The antibodies of this invention may be advantageously utilized in combination with other monoclonal or chimeric antibodies, or with lymphokines or hematopoietic growth factors (such as, e.g., IL-2, IL-3 and IL-7), for example, which serve to increase the number or activity of effector cells which interact with the antibodies.
The antibodies of the invention may be administered alone or in combination with other types of treatments (e.g., radiation therapy, chemotherapy, hormonal therapy, immunotherapy and anti-tumor agents). Generally, administration of products of a species origin or species reactivity (in the case of antibodies) that is the same species as that of the patient is preferred. Thus, in a preferred embodiment, human antibodies, fragments derivatives, analogs, or nucleic acids, are administered to a human patient for therapy or prophylaxis.
It is preferred to use high affinity and/or potent in vivo inhibiting and/or neutralizing antibodies against polypeptides or polynucleotides of the present invention, fragments or regions thereof, for both immunoassays directed to and therapy of disorders related to polynucleotides or polypeptides, including fragments thereof, of the present invention. Such antibodies, fragments, or regions, will preferably have an affinity for polynucleotides or polypeptides of the invention, including fragments thereof. Preferred binding affinities include those with a dissociation constant or Kd less than 5xc3x9710xe2x88x922 M, 10xe2x88x922 M, 5xc3x9710xe2x88x923 M, 10xe2x88x923 M, 5xc3x9710xe2x88x924 M, 10xe2x88x924 M, 5xc3x9710xe2x88x925 M, 10xe2x88x925 M, 5xc3x9710xe2x88x926 M, 10xe2x88x926 M, 5xc3x9710xe2x88x927 M, 10xe2x88x927 M, 5xc3x9710xe2x88x928 M, 10xe2x88x928 M, 5xc3x9710xe2x88x929 M, 10xe2x88x929 M, 5xc3x9710xe2x88x9210 M, 10xe2x88x9210 M, 5xc3x9710xe2x88x9211 M, 10xe2x88x9211 M, 5xc3x9710xe2x88x9212 M, 10xe2x88x9212 M, 5xc3x9710xe2x88x9213 M, 10xe2x88x9213 M, 5xc3x9710xe2x88x9214 M, 10xe2x88x9214 M, 5xc3x9710xe2x88x9215 M, and 10xe2x88x9215 M.
Gene Therapy
In a specific embodiment, nucleic acids comprising sequences encoding antibodies or functional derivatives thereof, are administered to treat, inhibit or prevent a disease or disorder associated with aberrant expression and/or activity of a polypeptide of the invention, by way of gene therapy. Gene therapy refers to therapy performed by the administration to a subject of an expressed or expressible nucleic acid. In this embodiment of the invention, the nucleic acids produce their encoded protein that mediates a therapeutic effect.
Any of the methods for gene therapy available in the art can be used according to the present invention. Exemplary methods are described below.
For general reviews of the methods of gene therapy, see Goldspiel et al., Clinical Pharmacy 12:488-505 (1993); Wu and Wu, Biotherapy 3:87-95 (1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217 (1993); May, TIBTECH 11(5):155-215 (1993). Methods commonly known in the art of recombinant DNA technology which can be used are described in Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley and Sons, NY (1993); and Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990).
In a preferred aspect, the compound comprises nucleic acid sequences encoding an antibody, said nucleic acid sequences being part of expression vectors that express the antibody or fragments or chimeric proteins or heavy or light chains thereof in a suitable host. In particular, such nucleic acid sequences have promoters operably linked to the antibody coding region, said promoter being inducible or constitutive, and, optionally, tissue-specific. In another particular embodiment, nucleic acid molecules are used in which the antibody coding sequences and any other desired sequences are flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for intrachromosomal expression of the antibody encoding nucleic acids (Koller and Smithies, Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438 (1989). In specific embodiments, the expressed antibody molecule is a single chain antibody; alternatively, the nucleic acid sequences include sequences encoding both the heavy and light chains, or fragments thereof, of the antibody.
Delivery of the nucleic acids into a patient may be either direct, in which case the patient is directly exposed to the nucleic acid or nucleic acid-carrying vectors, or indirect, in which case, cells are first transformed with the nucleic acids in vitro, then transplanted into the patient. These two approaches are known, respectively, as in vivo or ex vivo gene therapy.
In a specific embodiment, the nucleic acid sequences are directly administered in vivo, where it is expressed to produce the encoded product. This can be accomplished by any of numerous methods known in the art, e.g., by constructing them as part of an appropriate nucleic acid expression vector and administering it so that they become intracellular, e.g., by infection using defective or attenuated retrovirals or other viral vectors (see U.S. Pat. No. 4,980,286), or by direct injection of naked DNA, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, encapsulation in liposomes, microparticles, or microcapsules, or by administering them in linkage to a peptide which is known to enter the nucleus, by administering it in linkage to a ligand subject to receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)) (which can be used to target cell types specifically expressing the receptors), etc. In another embodiment, nucleic acid-ligand complexes can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation. In yet another embodiment, the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., PCT Publications WO 92/06180; WO 92/22635; WO92/20316; WO93/14188, WO 93/20221). Alternatively, the nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination (Koller and Smithies, Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438 (1989)).
In a specific embodiment, viral vectors that contains nucleic acid sequences encoding an antibody of the invention are used. For example, a retroviral vector can be used (see Miller et al., Meth. Enzymol. 217:581-599 (1993)). These retroviral vectors contain the components necessary for the correct packaging of the viral genome and integration into the host cell DNA. The nucleic acid sequences encoding the antibody to be used in gene therapy are cloned into one or more vectors, which facilitates delivery of the gene into a patient. More detail about retroviral vectors can be found in Boesen et al., Biotherapy 6:291-302 (1994), which describes the use of a retroviral vector to deliver the mdr1 gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy. Other references illustrating the use of retroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest. 93:644-651 (1994); Kiem et al., Blood 83:1467-1473 (1994); Salmons and Gunzberg, Human Gene Therapy 4:129-141 (1993); and Grossman and Wilson, Curr. Opin. in Genetics and Devel. 3:110-114 (1993).
Adenoviruses are other viral vectors that can be used in gene therapy. Adenoviruses are especially attractive vehicles for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, Current Opinion in Genetics and Development 3:499-503 (1993) present a review of adenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10 (1994) demonstrated the use of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus monkeys. Other instances of the use of adenoviruses in gene therapy can be found in Rosenfeld et al., Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143-155 (1992); Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT Publication WO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). In a preferred embodiment, adenovirus vectors are used.
Adeno-associated virus (AAV) has also been proposed for use in gene therapy (Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300 (1993); U.S. Pat. No. 5,436,146).
Another approach to gene therapy involves transferring a gene to cells in tissue culture by such methods as electroporation, lipofection, calcium phosphate mediated transfection, or viral infection. Usually, the method of transfer includes the transfer of a selectable marker to the cells. The cells are then placed under selection to isolate those cells that have taken up and are expressing the transferred gene. Those cells are then delivered to a patient.
In this embodiment, the nucleic acid is introduced into a cell prior to administration in vivo of the resulting recombinant cell. Such introduction can be carried out by any method known in the art, including but not limited to transfection, electroporation, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc. Numerous techniques are known in the art for the introduction of foreign genes into cells (see, e.g., Loeffler and Behr, Meth. Enzymol. 217:599-618 (1993); Cohen et al., Meth. Enzymol. 217:618-644 (1993); Cline, Pharmac. Ther. 29:69-92m (1985) and maybe used in accordance with the present invention, provided that the necessary developmental and physiological functions of the recipient cells are not disrupted. The technique should provide for the stable transfer of the nucleic acid to the cell, so that the nucleic acid is expressible by the cell and preferably heritable and expressible by its cell progeny.
The resulting recombinant cells can be delivered to a patient by various methods known in the art. Recombinant blood cells (e.g., hematopoietic stem or progenitor cells) are preferably administered intravenously. The amount of cells envisioned for use depends on the desired effect, patient state, etc., and can be determined by one skilled in the art.
Cells into which a nucleic acid can be introduced for purposes of gene therapy encompass any desired, available cell type, and include but are not limited to epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells, hepatocytes; blood cells such as Tlymphocytes, Blymphocytes, monocytes, macrophages, neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or progenitor cells, in particular hematopoietic stem or progenitor cells, e.g., as obtained from bone marrow, umbilical cord blood, peripheral blood, fetal liver, etc.
In a preferred embodiment, the cell used for gene therapy is autologous to the patient.
In an embodiment in which recombinant cells are used in gene therapy, nucleic acid sequences encoding an antibody are introduced into the cells such that they are expressible by the cells or their progeny, and the recombinant cells are then administered in vivo for therapeutic effect. In a specific embodiment, stem or progenitor cells are used. Any stem and/or progenitor cells which can be isolated and maintained in vitro can potentially be used in accordance with this embodiment of the present invention (see e.g. PCT Publication WO 94/08598; Stemple and Anderson, Cell 71:973-985 (1992); Rheinwald, Meth. Cell Bio. 21A:229 (1980); and Pittelkow and Scott, Mayo Clinic Proc. 61:771 (1986)).
In a specific embodiment, the nucleic acid to be introduced for purposes of gene therapy comprises an inducible promoter operably linked to the coding region, such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription.
Demonstration of Therapeutic or Prophylactic Activity
The compounds or pharmaceutical compositions of the invention are preferably tested in vitro, and then in vivo for the desired therapeutic or prophylactic activity, prior to use in humans. For example, in vitro assays to demonstrate the therapeutic or prophylactic utility of a compound or pharmaceutical composition include, the effect of a compound on a cell line or a patient tissue sample. The effect of the compound or composition on the cell line and/or tissue sample can be determined utilizing techniques known to those of skill in the art including, but not limited to, rosette formation assays and cell lysis assays. In accordance with the invention, in vitro assays which can be used to determine whether administration of a specific compound is indicated, include in vitro cell culture assays in which a patient tissue sample is grown in culture, and exposed to or otherwise administered a compound, and the effect of such compound upon the tissue sample is observed.
Therapeutic/Prophylactic Administration and Composition
The invention provides methods of treatment, inhibition and prophylaxis by administration to a subject of an effective amount of a compound or pharmaceutical composition of the invention, preferably an antibody of the invention. In a preferred aspect, the compound is substantially purified (e.g., substantially free from substances that limit its effect or produce undesired side-effects). The subject is preferably an animal, including but not limited to animals such as cows, pigs, horses, chickens, cats, dogs, etc., and is preferably a mammal, and most preferably human.
Formulations and methods of administration that can be employed when the compound comprises a nucleic acid or an immunoglobulin are described above; additional appropriate formulations and routes of administration can be selected from among those described herein below.
Various delivery systems are known and can be used to administer a compound of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432 (1987)), construction of a nucleic acid as part of a retroviral or other vector, etc. Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The compounds or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. In addition, it may be desirable to introduce the pharmaceutical compounds or compositions of the invention into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
In a specific embodiment, it may be desirable to administer the pharmaceutical compounds or compositions of the invention locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. Preferably, when administering a protein, including an antibody, of the invention, care must be taken to use materials to which the protein does not absorb.
In another embodiment, the compound or composition can be delivered in a vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.)
In yet another embodiment, the compound or composition can be delivered in a controlled release system. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); Saudek et al., N. Engl. J. Med. 321:574 (1989)). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol. Chem. 23:61 (1983); see also Levy et al., Science 228:190 (1985); During et al., Ann. Neurol. 25:351 (1989); Howard et al., J.Neurosurg. 71:105 (1989)). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)).
Other controlled release systems are discussed in the review by Langer (Science 249:1527-1533 (1990)).
In a specific embodiment where the compound of the invention is a nucleic acid encoding a protein, the nucleic acid can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see U.S. Pat. No. 4,980,286), or by direct injection, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al., Proc. Natl. Acad. Sci. USA 88:1864-1868 (1991)), etc. Alternatively, a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination.
The present invention also provides pharmaceutical compositions. Such compositions comprise a therapeutically effective amount of a compound, and a pharmaceutically acceptable carrier. In a specific embodiment, the term xe2x80x9cpharmaceutically acceptablexe2x80x9d means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term xe2x80x9ccarrierxe2x80x9d refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in xe2x80x9cRemington""s Pharmaceutical Sciencesxe2x80x9d by E. W. Martin. Such compositions will contain a therapeutically effective amount of the compound, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.
In a preferred embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
The compounds of the invention can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
The amount of the compound of the invention which will be effective in the treatment, inhibition and prevention of a disease or disorder associated with aberrant expression and/or activity of a polypeptide of the invention can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient""s circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.
For antibodies, the dosage administered to a patient is typically 0.1 mg/kg to 100 mg/kg of the patient""s body weight. Preferably, the dosage administered to a patient is between 0.1 mg/kg and 20 mg/kg of the patient""s body weight, more preferably 1 mg/kg to 10 mg/kg of the patient""s body weight. Generally, human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides. Thus, lower dosages of human antibodies and less frequent administration is often possible. Further, the dosage and frequency of administration of antibodies of the invention may be reduced by enhancing uptake and tissue penetration (e.g., into the brain) of the antibodies by modifications such as, for example, lipidation.
The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.
Diagnosis and Imaging
Labeled antibodies, and derivatives and analogs thereof, which specifically bind to a polypeptide of interest can be used for diagnostic purposes to detect, diagnose, or monitor diseases, disorders, and/or conditions associated with the aberrant expression and/or activity of a polypeptide of the invention. The invention provides for the detection of aberrant expression of a polypeptide of interest, comprising (a) assaying the expression of the polypeptide of interest in cells or body fluid of an individual using one or more antibodies specific to the polypeptide interest and (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of aberrant expression.
The invention provides a diagnostic assay for diagnosing a disorder, comprising (a) assaying the expression of the polypeptide of interest in cells or body fluid of an individual using one or more antibodies specific to the polypeptide interest and (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of a particular disorder. With respect to cancer, the presence of a relatively high amount of transcript in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.
Antibodies of the invention can be used to assay protein levels in a biological sample using classical immunohistological methods known to those of skill in the art (e.g., see Jalkanen, et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, et al., J. Cell. Biol. 105:3087-3096 (1987)). Other antibody-based methods useful for detecting protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels are known in the art and include enzyme labels, such as, glucose oxidase; radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99Tc); luminescent labels, such as luminol; and fluorescent labels, such as fluorescein and rhodamine, and biotin.
One aspect of the invention is the detection and diagnosis of a disease or disorder associated with aberrant expression of a polypeptide of interest in an animal, preferably a mammal and most preferably a human. In one embodiment, diagnosis comprises: a) administering (for example, parenterally, subcutaneously, or intraperitoneally) to a subject an effective amount of a labeled molecule which specifically binds to the polypeptide of interest; b) waiting for a time interval following the administering for permitting the labeled molecule to preferentially concentrate at sites in the subject where the polypeptide is expressed (and for unbound labeled molecule to be cleared to background level); c) determining background level; and d) detecting the labeled molecule in the subject, such that detection of labeled molecule above the background level indicates that the subject has a particular disease or disorder associated with aberrant expression of the polypeptide of interest. Background level can be determined by various methods including, comparing the amount of labeled molecule detected to a standard value previously determined for a particular system.
It will be understood in the art that the size of the subject and the imaging system used will determine the quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope moiety, for a human subject, the quantity of radioactivity injected will normally range from about 5 to 20 millicuries of 99mTc. The labeled antibody or antibody fragment will then preferentially accumulate at the location of cells which contain the specific protein. In vivo tumor imaging is described in S. W. Burchiel et al., xe2x80x9cImmunopharmacokinetics of Radiolabeled Antibodies and Their Fragiments.xe2x80x9d (Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, S. W. Burchiel and B. A. Rhodes, eds., Masson Publishing Inc. (1982).
Depending on several variables, including the type of label used and the mode of administration, the time interval following the administration for permitting the labeled molecule to preferentially concentrate at sites in the subject and for unbound labeled molecule to be cleared to background level is 6 to 48 hours or 6 to 24 hours or 6 to 12 hours. In another embodiment the time interval following administration is 5 to 20 days or 5 to 10 days.
In an embodiment, monitoring of the disease or disorder is carried out by repeating the method for diagnosing the disease or disease, for example, one month after initial diagnosis, six months after initial diagnosis, one year after initial diagnosis, etc.
Presence of the labeled molecule can be detected in the patient using methods known in the art for in vivo scanning. These methods depend upon the type of label used. Skilled artisans will be able to determine the appropriate method for detecting a particular label. Methods and devices that may be used in the diagnostic methods of the invention include, but are not limited to, computed tomography (CT), whole body scan such as position emission tomography (PET), magnetic resonance imaging (MRI), and sonography.
In a specific embodiment, the molecule is labeled with a radioisotope and is detected in the patient using a radiation responsive surgical instrument (Thurston et al., U.S. Pat. No. 5,441,050). In another embodiment, the molecule is labeled with a fluorescent compound and is detected in the patient using a fluorescence responsive scanning instrument. In another embodiment, the molecule is labeled with a positron emitting metal and is detected in the patent using positron emission-tomography. In yet another embodiment, the molecule is labeled with a paramagnetic label and is detected in a patient using magnetic resonance imaging (MRI).
Kits
The present invention provides kits that can be used in the above methods. In one embodiment, a kit comprises an antibody of the invention, preferably a purified antibody, in one or more containers. In a specific embodiment, the kits of the present invention contain a substantially isolated polypeptide comprising an epitope which is specifically immunoreactive with an antibody included in the kit. Preferably, the kits of the present invention further comprise a control antibody which does not react with the polypeptide of interest. In another specific embodiment, the kits of the present invention contain a means for detecting the binding of an antibody to a polypeptide of interest (e.g., the antibody may be conjugated to a detectable substrate such as a fluorescent compound, an enzymatic substrate, a radioactive compound or a luminescent compound, or a second antibody which recognizes the first antibody may be conjugated to a detectable substrate).
In another specific embodiment of the present invention, the kit is a diagnostic kit for use in screening serum containing antibodies specific against proliferative and/or cancerous polynucleotides and polypeptides. Such a kit may include a control antibody that does not react with the polypeptide of interest. Such a kit may include a substantially isolated polypeptide antigen comprising an epitope which is specifically immunoreactive with at least one anti-polypeptide antigen antibody. Further, such a kit includes means for detecting the binding of said antibody to the antigen (e.g., the antibody may be conjugated to a fluorescent compound such as fluorescein or rhodamine which can be detected by flow cytometry). In specific embodiments, the kit may include a recombinantly produced or chemically synthesized polypeptide antigen. The polypeptide antigen of the kit may also be attached to a solid support.
In a more specific embodiment the detecting means of the above-described kit includes a solid support to which said polypeptide antigen is attached. Such a kit may also include a non-attached reporter-labeled anti-human antibody. In this embodiment, binding of the antibody to the polypeptide antigen can be detected by binding of the said reporter-labeled antibody.
In an additional embodiment, the invention includes a diagnostic kit for use in screening serum containing antigens of the polypeptide of the invention. The diagnostic kit includes a substantially isolated antibody specifically immunoreactive with polypeptide or polynucleotide antigens, and means for detecting the binding of the polynucleotide or polypeptide antigen to the antibody. In one embodiment, the antibody is attached to a solid support. In a specific embodiment, the antibody may be a monoclonal antibody. The detecting means of the kit may include a second, labeled monoclonal antibody. Alternatively, or in addition, the detecting means may include a labeled, competing antigen.
In one diagnostic configuration, test serum is reacted with a solid phase reagent having a surface-bound antigen obtained by the methods of the present invention. After binding with specific antigen antibody to the reagent and removing unbound serum components by washing, the reagent is reacted with reporter-labeled anti-human antibody to bind reporter to the reagent in proportion to the amount of bound anti-antigen antibody on the solid support. The reagent is again washed to remove unbound labeled antibody, and the amount of reporter associated with the reagent is determined. Typically, the reporter is an enzyme which is detected by incubating the solid phase in the presence of a suitable fluorometric, luminescent or colorimetric substrate (Sigma, St. Louis, Mo.).
The solid surface reagent in the above assay is prepared by known techniques for attaching protein material to solid support material, such as polymeric beads, dip sticks, 96-well plate or filter material. These attachment methods generally include non-specific adsorption of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activated carboxyl, hydroxyl, or aldehyde group. Alternatively, streptavidin coated plates can be used in conjunction with biotinylated antigen(s).
Thus, the invention provides an assay system or kit for carrying out this diagnostic method. The kit generally includes a support with surface-bound recombinant antigens, and a reporter-labeled anti-human antibody for detecting surface-bound anti-antigen antibody.
Fusion Proteins
Any polypeptide of the present invention can be used to generate fusion proteins. For example, the polypeptide of the present invention, when fused to a second protein, can be used as an antigenic tag. Antibodies raised against the polypeptide of the present invention can be used to indirectly detect the second protein by binding to the polypeptide. Moreover, because secreted proteins target cellular locations based on trafficking signals, the polypeptides of the present invention can be used as targeting molecules once fused to other proteins.
Examples of domains that can be fused to polypeptides of the present invention include not only heterologous signal sequences, but also other heterologous functional regions. The fusion does not necessarily need to be direct, but may occur through linker sequences.
Moreover, fusion proteins may also be engineered to improve characteristics of the polypeptide of the present invention. For instance, a region of additional amino acids, particularly charged amino acids, may be added to the N-terminus of the polypeptide to improve stability and persistence during purification from the host cell or subsequent handling and storage. Also, peptide moieties may be added to the polypeptide to facilitate purification. Such regions may be removed prior to final preparation of the polypeptide. The addition of peptide moieties to facilitate handling of polypeptides are familiar and routine techniques in the art.
Moreover, polypeptides of the present invention, including fragments, and specifically epitopes, can be combined with parts of the constant domain of immunoglobulins (IgA, IgE, IgG, IgM) or portions thereof (CH1, CH2, CH3, and any combination thereof, including both entire domains and portions thereof), resulting in chimeric polypeptides. These fusion proteins facilitate purification and show an increased half-life in vivo. One reported example describes chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins. (EP A 394,827; Traunecker et al., Nature 331:84-86 (1988).) Fusion proteins having disulfide-linked dimeric structures (due to the IgG) can also be more efficient in binding and neutralizing other molecules, than the monomeric secreted protein or protein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964 (1995).) Polynucleotides comprising or alternatively consisting of nucleic acids which encode these fusion proteins are also encompassed by the invention.
Similarly, EP-A-O 464 533 (Canadian counterpart 2045869) discloses fusion proteins comprising various portions of constant region of immunoglobulin molecules together with another human protein or part thereof. In many cases, the Fc part in a fusion protein is beneficial in therapy and diagnosis, and thus can result in, for example, improved pharmacokinetic properties. (EP-A 0232 262.) Alternatively, deleting the Fc part after the fusion protein has been expressed, detected, and purified, would be desired. For example, the Fc portion may hinder therapy and diagnosis if the fusion protein is used as an antigen for immunizations. In drug discovery, for example, human proteins, such as hIL-5, have been fused with Fc portions for the purpose of high-throughput screening assays to identify antagonists of hIL-5. (See, D. Bennett et al., J. Molecular Recognition 8:52-58 (1995); K. Johanson et al., J. Biol. Chem. 270:9459-9471 (1995).)
Moreover, the polypeptides of the present invention can be fused to marker sequences, such as a peptide which facilitates purification of the fused polypeptide. In preferred embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance, hexa-histidine provides for convenient purification of the fusion protein. Another peptide tag useful for purification, the xe2x80x9cHAxe2x80x9d tag, corresponds to an epitope derived from the influenza hemagglutinin protein. (Wilson et al., Cell 37:767 (1984).)
Thus, any of these above fusions can be engineered using the polynucleotides or the polypeptides of the present invention.
Vectors, Host Cells, and Protein Production
The present invention also relates to vectors containing the polynucleotide of the present invention, host cells, and the production of polypeptides by recombinant techniques. The vector may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.
The polynucleotides may be joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.
The polynucleotide insert should be operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and tac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.
As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase, G418 or neomycin resistance for eukaryotic cell culture and tetracycline, kanamycin or ampicillin resistance genes for culturing in E. coli and other bacteria. Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC(copyright) Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and conditions for the above-described host cells are known in the art.
Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Preferred expression vectors for use in yeast systems include, but are not limited to pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalph, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, pPIC9K, and PAO815 (all available from Invitrogen, Carlbad, Calif.). Other suitable vectors will be readily apparent to the skilled artisan.
Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides of the present invention may in fact be expressed by a host cell lacking a recombinant vector.
A polypeptide of this invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography (xe2x80x9cHPLCxe2x80x9d) is employed for purification.
Polypeptides of the present invention, and preferably the secreted form, can also be recovered from: products purified from natural sources, including bodily fluids, tissues and cells, whether directly isolated or cultured; products of chemical synthetic procedures; and products produced by recombinant techniques from a prokaryotic or eukaryotic host, including, for example, bacterial, yeast, higher plant, insect, and mammalian cells. Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. In addition, polypeptides of the invention may also include an initial modified methionine residue, in some cases as a result of host-mediated processes. Thus, it is well known in the art that the N-terminal methionine encoded by the translation initiation codon generally is removed with high efficiency from any protein after translation in all eukaryotic cells. While the N-terminal methionine on most proteins also is efficiently removed in most prokaryotes, for some proteins, this prokaryotic removal process is inefficient, depending on the nature of the amino acid to which the N-terminal methionine is covalently linked.
In one embodiment, the yeast Pichia pastoris is used to express the polypeptide of the present invention in a eukaryotic system. Pichia pastoris is a methylotrophic yeast which can metabolize methanol as its sole carbon source. A main step in the methanol metabolization pathway is the oxidation of methanol to formaldehyde using O2. This reaction is catalyzed by the enzyme alcohol oxidase. In order to metabolize methanol as its sole carbon source, Pichia pastoris must generate high levels of alcohol oxidase due, in part, to the relatively low affinity of alcohol oxidase for O2. Consequently, in a growth medium depending on methanol as a main carbon source, the promoter region of one of the two alcohol oxidase genes (AOX1) is highly active. In the presence of methanol, alcohol oxidase produced from the AOX1 gene comprises up to approximately 30% of the total soluble protein in Pichia pastoris. See, Ellis, S. B., et al, Mol. Cell. Biol. 5:1111-21 (1985); Koutz, P. J. et al., Yeast 5:167-77 (1989); Tschopp, J. F., et al., Nucl. Acids Res. 15:3859-76 (1987). Thus, a heterologous coding sequence, such as, for example, a polynucleotide of the present invention, under the transcriptional regulation of all or part of the AOX1 regulatory sequence is expressed at exceptionally high levels in Pichia yeast grown in the presence of methanol.
In one example, the plasmid vector pPIC9K is used to express DNA encoding a polypeptide of the invention, as set forth herein, in a Pichea yeast system essentially as described in xe2x80x9cPichia Protocols: Methods in Molecular Biology,xe2x80x9d D. R. Higgins and J. Cregg, eds. The Humana Press, Totowa, N.J., 1998. This expression vector allows expression and secretion of a protein of the invention by virtue of the strong AOX1 promoter linked to the Pichia pastoris alkaline phosphatase (PHO) secretory signal peptide (i.e., leader) located upstream of a multiple cloning site.
Many other yeast vectors could be used in place of pPIC9K, such as, pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalpha, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, and PAO815, as one skilled in the art would readily appreciate, as long as the proposed expression construct provides appropriately located signals for transcription, translation, secretion (if desired), and the like, including an in-frame AUG as required.
In another embodiment, high-level expression of a heterologous coding sequence, such as, for example, a polynucleotide of the present invention, may be achieved by cloning the heterologous polynucleotide of the invention into an expression vector such as, for example, pGAPZ or pGAPZalpha, and growing the yeast culture in the absence of methanol.
In addition to encompassing host cells containing the vector constructs discussed herein, the invention also encompasses primary, secondary, and immortalized host cells of vertebrate origin, particularly mammalian origin, that have been engineered to delete or replace endogenous genetic material (e.g., coding sequence), and/or to include genetic material (e.g., heterologous polynucleotide sequences) that is operably associated with the polynucleotides of the invention, and which activates, alters, and/or amplifies endogenous polynucleotides. For example, techniques known in the art may be used to operably associate heterologous control regions (e.g., promoter and/or enhancer) and endogenous polynucleotide sequences via homologous recombination, resulting in the formation of a new transcription unit (see, e.g., U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; U.S. Pat. No. 5,733,761, issued Mar. 31, 1998; International Publication No. WO 96/29411, published Sep. 26, 1996; International Publication No. WO 94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al., Nature 342:435-438 (1989), the disclosures of each of which are incorporated by reference in their entireties).
In addition, polypeptides of the invention can be chemically synthesized using techniques known in the art (e.g., see Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman and Co., N.Y., and Hunkapiller et al., Nature, 310:105-111 (1984)). For example, a polypeptide corresponding to a fragment of a polypeptide sequence of the invention can be synthesized by use of a peptide synthesizer. Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the polypeptide sequence. Non-classical amino acids include, but are not limited to, to the D-isomers of the common amino acids, 2,4-diaminobutyric acid, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, g-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, b-alanine, fluoro-amino acids, designer amino acids such as b-methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).
The invention encompasses polypeptides which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc. Any of numerous chemical modifications may be carried out by known techniques, including but not limited, to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4; acetylation, formylation, oxidation, reduction; metabolic synthesis in the presence of tunicamycin; etc.
Additional post-translational modifications encompassed by the invention include, for example, e.g., N-linked or O-linked carbohydrate chains, processing of N-terminal or C-terminal ends), attachment of chemical moieties to the amino acid backbone, chemical modifications of N-linked or O-linked carbohydrate chains, and addition or deletion of an N-terminal methionine residue as a result of procaryotic host cell expression. The polypeptides may also be modified with a detectable label, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the protein.
Also provided by the invention are chemically modified derivatives of the polypeptides of the invention which may provide additional advantages such as increased solubility, stability and circulating time of the polypeptide, or decreased immunogenicity (see U.S. Pat. No. 4,179,337). The chemical moieties for derivitization may be selected from water soluble polymers such as polyethylene glycol, ethylene glycol/propylene glycol copolymers, carboxymethylcellulose, dextran, polyvinyl alcohol and the like. The polypeptides may be modified at random positions within the molecule, or at predetermined positions within the molecule and may include one, two, three or more attached chemical moieties.
The polymer may be of any molecular weight, and may be branched or unbranched. For polyethylene glycol, the preferred molecular weight is between about 1 kDa and about 100 kDa (the term xe2x80x9caboutxe2x80x9d indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight) for ease in handling and manufacturing. Other sizes may be used, depending on the desired therapeutic profile (e.g., the duration of sustained release desired, the effects, if any on biological activity, the ease in handling, the degree or lack of antigenicity and other known effects of the polyethylene glycol to a therapeutic protein or analog). For example, the polyethylene glycol may have an average molecular weight of about 200, 500, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10,000, 10,500, 11,000, 11,500, 12,000, 12,500, 13,000, 13,500, 14,000, 14,500, 15,000, 15,500, 16,000, 16,500, 17,000, 17,500, 18,000, 18,500, 19,000, 19,500, 20,000, 25,000, 30,000, 35,000, 40,000, 50,000, 55,000, 60,000, 65,000, 70,000, 75,000, 80,000, 85,000, 90,000, 95,000, or 100,000 kDa.
As noted above, the polyethylene glycol may have a branched structure. Branched polyethylene glycols are described, for example, in U.S. Pat. No. 5,643,575; Morpurgo et al., Appl. Biochem. Biotechnol. 56:59-72 (1996); Vorobjev et al., Nucleosides Nucleotides 18:2745-2750 (1999); and Caliceti et al., Bioconjug. Chem. 10:638-646 (1999), the disclosures of each of which are incorporated herein by reference.
The polyethylene glycol molecules (or other chemical moieties) should be attached to the protein with consideration of effects on functional or antigenic domains of the protein. There are a number of attachment methods available to those skilled in the art, e.g., EP 0 401 384, herein incorporated by reference (coupling PEG to G-CSF), see also Malik et al., Exp. Hematol. 20:1028-1035 (1992) (reporting pegylation of GM-CSF using tresyl chloride). For example, polyethylene glycol may be covalently bound through amino acid residues via a reactive group, such as, a free amino or carboxyl group. Reactive groups are those to which an activated polyethylene glycol molecule may be bound. The amino acid residues having a free amino group may include lysine residues and the N-terminal amino acid residues; those having a free carboxyl group may include aspartic acid residues glutamic acid residues and the C-terminal amino acid residue. Sulfhydryl groups may also be used as a reactive group for attaching the polyethylene glycol molecules. Preferred for therapeutic purposes is attachment at an amino group, such as attachment at the N-terminus or lysine group.
As suggested above, polyethylene glycol may be attached to proteins via linkage to any of a number of amino acid residues. For example, polyethylene glycol can be linked to a proteins via covalent bonds to lysine, histidine, aspartic acid, glutamic acid, or cysteine residues. One or more reaction chemistries may be employed to attach polyethylene glycol to specific amino acid residues (e.g., lysine, histidine, aspartic acid, glutamic acid, or cysteine) of the protein or to more than one type of amino acid residue (e.g., lysine, histidine, aspartic acid, glutamic acid, cysteine and combinations thereof) of the protein.
One may specifically desire proteins chemically modified at the N-terminus. Using polyethylene glycol as an illustration of the present composition, one may select from a variety of polyethylene glycol molecules (by molecular weight, branching, etc.), the proportion of polyethylene glycol molecules to protein (polypeptide) molecules in the reaction mix, the type of pegylation reaction to be performed, and the method of obtaining the selected N-terminally pegylated protein. The method of obtaining the N-terminally pegylated preparation (i.e., separating this moiety from other monopegylated moieties if necessary) may be by purification of the N-terminally pegylated material from a population of pegylated protein molecules. Selective proteins chemically modified at the N-terminus modification may be accomplished by reductive alkylation which exploits differential reactivity of different types of primary amino groups (lysine versus the N-terminal) available for derivatization in a particular protein. Under the appropriate reaction conditions, substantially selective derivatization of the protein at the N-terminus with a carbonyl group containing polymer is achieved.
As indicated above, pegylation of the proteins of the invention may be accomplished by any number of means. For example, polyethylene glycol may be attached to the protein either directly or by an intervening linker. Linkerless systems for attaching polyethylene glycol to proteins are described in Delgado et al., Crit. Rev. Thera. Drug Carrier Sys. 9:249-304 (1992); Francis et al., Intern. J. of Hematol. 68:1-18 (1998); U.S. Pat. Nos. 4,002,531; 5,349,052; WO 95/06058; and WO 98/32466, the disclosures of each of which are incorporated herein by reference.
One system for attaching polyethylene glycol directly to amino acid residues of proteins without an intervening linker employs tresylated MPEG, which is produced by the modification of monmethoxy polyethylene glycol (MPEG) using tresylchloride (ClSO2CH2CF3). Upon reaction of protein with tresylated MPEG, polyethylene glycol is directly attached to amine groups of the protein. Thus, the invention includes protein-polyethylene glycol conjugates produced by reacting proteins of the invention with a polyethylene glycol molecule having a 2,2,2-trifluoreothane sulphonyl group.
Polyethylene glycol can also be attached to proteins using a number of different intervening linkers. For example, U.S. Pat. No. 5,612,460, the entire disclosure of which is incorporated herein by reference, discloses urethane linkers for connecting polyethylene glycol to proteins. Protein-polyethylene glycol conjugates wherein the polyethylene glycol is attached to the protein by a linker can also be produced by reaction of proteins with compounds such as MPEG-succinimidylsuccinate, MPEG activated with 1,1xe2x80x2-carbonyldiimidazole, MPEG-2,4,5-trichloropenylcarbonate, MPEG-p-nitrophenolcarbonate, and various MPEG-succinate derivatives. A number additional polyethylene glycol derivatives and reaction chemistries for attaching polyethylene glycol to proteins are described in WO 98/32466, the entire disclosure of which is incorporated herein by reference. Pegylated protein products produced using the reaction chemistries set out herein are included within the scope of the invention.
The number of polyethylene glycol moieties attached to each protein of the invention (i.e., the degree of substitution) may also vary. For example, the pegylated proteins of the invention may be linked, on average, to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, or more polyethylene glycol molecules. Similarly, the average degree of substitution within ranges such as 1-3, 2-4, 3-5, 4-6, 5-7, 6-8, 7-9, 8-10, 9-11, 10-12, 11-13, 12-14, 13-15, 14-16, 15-17, 16-18, 17-19, or 18-20 polyethylene glycol moieties per protein molecule. Methods for determining the degree of substitution are discussed, for example, in Delgado et al., Crit. Rev. Thera. Drug Carrier Sys. 9:249-304 (1992).
The polypeptides of the invention may be in monomers or multimers (i.e., dimers, trimers, tetramers and higher multimers). Accordingly, the present invention relates to monomers and multimers of the polypeptides of the invention, their preparation, and compositions (preferably, Therapeutics) containing them. In specific embodiments, the polypeptides of the invention are monomers, dimers, trimers or tetramers. In additional embodiments, the multimers of the invention are at least dimers, at least trimers, or at least tetramers.
Multimers encompassed by the invention may be homomers or heteromers. As used herein, the term homomer, refers to a multimer containing only polypeptides corresponding to the amino acid sequence of SEQ ID NO:Y or encoded by the cDNA contained in a deposited clone (including fragments, variants, splice variants, and fusion proteins, corresponding to these polypeptides as described herein). These homomers may contain polypeptides having identical or different amino acid sequences. In a specific embodiment, a homomer of the invention is a multimer containing only polypeptides having an identical amino acid sequence. In another specific embodiment, a homomer of the invention is a multimer containing polypeptides having different amino acid sequences. In specific embodiments, the multimer of the invention is a homodimer (e.g., containing polypeptides having identical or different amino acid sequences) or a homotrimer (e.g., containing polypeptides having identical and/or different amino acid sequences). In additional embodiments, the homomeric multimer of the invention is at least a homodimer, at least a homotrimer, or at least a homotetramer.
As used herein, the term heteromer refers to a multimer containing one or more heterologous polypeptides (i.e., polypeptides of different proteins) in addition to the polypeptides of the invention. In a specific embodiment, the multimer of the invention is a heterodimer, a heterotrimer, or a heterotetramer. In additional embodiments, the heteromeric multimer of the invention is at least a heterodimer, at least a heterotrimer, or at least a heterotetramer.
Multimers of the invention may be the result of hydrophobic, hydrophilic, ionic and/or covalent associations and/or may be indirectly linked, by for example, liposome formation. Thus, in one embodiment, multimers of the invention, such as, for example, homodimers or homotrimers, are formed when polypeptides of the invention contact one another in solution. In another embodiment, heteromultimers of the invention, such as, for example, heterotrimers or heterotetramers, are formed when polypeptides of the invention contact antibodies to the polypeptides of the invention (including antibodies to the heterologous polypeptide sequence in a fusion protein of the invention) in solution. In other embodiments, multimers of the invention are formed by covalent associations with and/or between the polypeptides of the invention. Such covalent associations may involve one or more amino acid residues contained in the polypeptide sequence (e.g., that recited in the sequence listing, or contained in the polypeptide encoded by a deposited clone). In one instance, the covalent associations are cross-linking between cysteine residues located within the polypeptide sequences which interact in the native (i.e., naturally occurring) polypeptide. In another instance, the covalent associations are the consequence of chemical or recombinant manipulation. Alternatively, such covalent associations may involve one or more amino acid residues contained in the heterologous polypeptide sequence in a fusion protein of the invention.
In one example, covalent associations are between the heterologous sequence contained in a fusion protein of the invention (see, e.g., U.S. Pat. No. 5,478,925). In a specific example, the covalent associations are between the heterologous sequence contained in an Fc fusion protein of the invention (as described herein). In another specific example, covalent associations of fusion proteins of the invention are between heterologous polypeptide sequence from another protein that is capable of forming covalently associated multimers, such as for example, oseteoprotegerin (see, e.g., International Publication NO: WO 98/49305, the contents of which are herein incorporated by reference in its entirety). In another embodiment, two or more polypeptides of the invention are joined through peptide linkers. Examples include those peptide linkers described in U.S. Pat. No. 5,073,627 (hereby incorporated by reference). Proteins comprising multiple polypeptides of the invention separated by peptide linkers may be produced using conventional recombinant DNA technology.
Another method for preparing multimer polypeptides of the invention involves use of polypeptides of the invention fused to a leucine zipper or isoleucine zipper polypeptide sequence. Leucine zipper and isoleucine zipper domains are polypeptides that promote multimerization of the proteins in which they are found. Leucine zippers were originally identified in several DNA-binding proteins (Landschulz et al., Science 240:1759, (1988)), and have since been found in a variety of different proteins. Among the known leucine zippers are naturally occurring peptides and derivatives thereof that dimerize or trimerize. Examples of leucine zipper domains suitable for producing soluble multimeric proteins of the invention are those described in PCT application WO 94/10308, hereby incorporated by reference. Recombinant fusion proteins comprising a polypeptide of the invention fused to a polypeptide sequence that dimerizes or trimerizes in solution are expressed in suitable host cells, and the resulting soluble multimeric fusion protein is recovered from the culture supernatant using techniques known in the art.
Trimeric polypeptides of the invention may offer the advantage of enhanced biological activity. Preferred leucine zipper moieties and isoleucine moieties are those that preferentially form trimers. One example is a leucine zipper derived from lung surfactant protein D (SPD), as described in Hoppe et al. (FEBS Letters 344:191, (1994)) and in U.S. patent application Ser. No. 08/446,922, hereby incorporated by reference. Other peptides derived from naturally occurring trimeric proteins may be employed in preparing trimeric polypeptides of the invention.
In another example, proteins of the invention are associated by interactions between Flag(copyright) polypeptide sequence contained in fusion proteins of the invention containing Flag(copyright) polypeptide sequence. In a further embodiment, associations proteins of the invention are associated by interactions between heterologous polypeptide sequence contained in Flag(copyright) fusion proteins of the invention and anti-Flag(copyright) antibody.
The multimers of the invention may be generated using chemical techniques known in the art. For example, polypeptides desired to be contained in the multimers of the invention may be chemically cross-linked using linker molecules and linker molecule length optimization techniques known in the art (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Additionally, multimers of the invention may be generated using techniques known in the art to form one or more inter-molecule cross-links between the cysteine residues located within the sequence of the polypeptides desired to be contained in the multimer (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Further, polypeptides of the invention may be routinely modified by the addition of cysteine or biotin to the C terminus or N-terminus of the polypeptide and techniques known in the art may be applied to generate multimers containing one or more of these modified polypeptides (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). Additionally, techniques known in the art may be applied to generate liposomes containing the polypeptide components desired to be contained in the multimer of the invention (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety).
Alternatively, multimers of the invention may be generated using genetic engineering techniques known in the art. In one embodiment, polypeptides contained in multimers of the invention are produced recombinantly using fusion protein technology described herein or otherwise known in the art (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). In a specific embodiment, polynucleotides coding for a homodimer of the invention are generated by ligating a polynucleotide sequence encoding a polypeptide of the invention to a sequence encoding a linker polypeptide and then further to a synthetic polynucleotide encoding the translated product of the polypeptide in the reverse orientation from the original C-terminus to the N-terminus (lacking the leader sequence) (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety). In another embodiment, recombinant techniques described herein or otherwise known in the art are applied to generate recombinant polypeptides of the invention which contain a transmembrane domain (or hyrophobic or signal peptide) and which can be incorporated by membrane reconstitution techniques into liposomes (see, e.g., U.S. Pat. No. 5,478,925, which is herein incorporated by reference in its entirety).
Uses of the Polynucleotides
Each of the polynucleotides identified herein can be used in numerous ways as reagents. The following description should be considered exemplary and utilizes known techniques.
The polynucleotides of the present invention are useful for chromosome identification. There exists an ongoing need to identify new chromosome markers, since few chromosome marking reagents, based on actual sequence data (repeat polymorphisms), are presently available. Each polynucleotide of the present invention can be used as a chromosome marker.
Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp) from the sequences shown in SEQ ID NO:X. Primers can be selected using computer analysis so that primers do not span more than one predicted exon in the genomic DNA. These primers are then used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the SEQ ID NO:X will yield an amplified fragment.
Similarly, somatic hybrids provide a rapid method of PCR mapping the polynucleotides to particular chromosomes. Three or more clones can be assigned per day using a single thermal cycler. Moreover, sublocalization of the polynucleotides can be achieved with panels of specific chromosome fragments. Other gene mapping strategies that can be used include in situ hybridization, prescreening with labeled flow-sorted chromosomes, preselection by hybridization to construct chromosome specific-cDNA libraries and computer mapping techniques (See, e.g., Shuler, Trends Biotechnol 16:456-459 (1998) which is hereby incorporated by reference in its entirety).
Precise chromosomal location of the polynucleotides can also be achieved using fluorescence in situ hybridization (FISH) of a metaphase chromosomal spread. This technique uses polynucleotides as short as 500 or 600 bases; however, polynucleotides 2,000-4,000 bp are preferred. For a review of this technique, see Verma et al., xe2x80x9cHuman Chromosomes: a Manual of Basic Techniques,xe2x80x9d Pergamon Press, New York (1988).
For chromosome mapping, the polynucleotides can be used individually (to mark a single chromosome or a single site on that chromosome) or in panels (for marking multiple sites and/or multiple chromosomes).
The polynucleotides of the present invention would likewise be useful for radiation hybrid mapping, HAPPY mapping, and long range restriction mapping. For a review of these techniques and others known in the art, see, e.g., Dear, xe2x80x9cGenome Mapping: A Practical Approach,xe2x80x9d IRL Press at Oxford University Press, London (1997); Aydin, J. Mol. Med. 77:691-694 (1999); Hacia et al., Mol. Psychiatry 3:483-492 (1998); Herrick et al., Chromosome Res. 7:409-423 (1999); Hamilton et al., Methods Cell Biol. 62:265-280 (2000); and/or Ott, J. Hered. 90:68-70 (1999) each of which is hereby incorporated by reference in its entirety.
Once a polynucleotide has been mapped to a precise chromosomal location, the physical position of the polynucleotide can be used in linkage analysis. Linkage analysis establishes coinheritance between a chromosomal location and presentation of a particular disease. (Disease mapping data are found, for example, in V. McKusick, Mendelian Inheritance in Man (available on line through Johns Hopkins University Welch Medical Library).) Assuming 1 megabase mapping resolution and one gene per 20 kb, a cDNA precisely localized to a chromosomal region associated with the disease could be one of 50-500 potential causative genes.
Thus, once coinheritance is established, differences in the polynucleotide and the corresponding gene between affected and unaffected individuals can be examined. First, visible structural alterations in the chromosomes, such as deletions or translocations, are examined in chromosome spreads or by PCR. If no structural alterations exist, the presence of point mutations are ascertained. Mutations observed in some or all affected individuals, but not in normal individuals, indicates that the mutation may cause the disease. However, complete sequencing of the polypeptide and the corresponding gene from several normal individuals is required to distinguish the mutation from a polymorphism. If a new polymorphism is identified, this polymorphic polypeptide can be used for further linkage analysis.
Furthermore, increased or decreased expression of the gene in affected individuals as compared to unaffected individuals can be assessed using polynucleotides of the present invention. Any of these alterations (altered expression, chromosomal rearrangement, or mutation) can be used as a diagnostic or prognostic marker.
Thus, the invention also provides a diagnostic method useful during diagnosis of a disorder, involving measuring the expression level of polynucleotides of the present invention in cells or body fluid from an individual and comparing the measured gene expression level with a standard level of polynucleotide expression level, whereby an increase or decrease in the gene expression level compared to the standard is indicative of a disorder.
In still another embodiment, the invention includes a kit for analyzing samples for the presence of proliferative and/or cancerous polynucleotides derived from a test subject. In a general embodiment, the kit includes at least one polynucleotide probe containing a nucleotide sequence that will specifically hybridize with a polynucleotide of the present invention and a suitable container. In a specific embodiment, the kit includes two polynucleotide probes defining an internal region of the polynucleotide of the present invention, where each probe has one strand containing a 31xe2x80x2mer-end internal to the region. In a further embodiment, the probes may be useful as primers for polymerase chain reaction amplification.
Where a diagnosis of a disorder, has already been made according to conventional methods, the present invention is useful as a prognostic indicator, whereby patients exhibiting enhanced or depressed polynucleotide of the present invention expression will experience a worse clinical outcome relative to patients expressing the gene at a level nearer the standard level.
By xe2x80x9cmeasuring the expression level of polynucleotide of the present inventionxe2x80x9d is intended qualitatively or quantitatively measuring or estimating the level of the polypeptide of the present invention or the level of the mRNA encoding the polypeptide in a first biological sample either directly (e.g., by determining or estimating absolute protein level or mRNA level) or relatively (e.g., by comparing to the polypeptide level or mRNA level in a second biological sample). Preferably, the polypeptide level or mRNA level in the first biological sample is measured or estimated and compared to a standard polypeptide level or mRNA level, the standard being taken from a second biological sample obtained from an individual not having the disorder or being determined by averaging levels from a population of individuals not having a disorder. As will be appreciated in the art, once a standard polypeptide level or mRNA level is known, it can be used repeatedly as a standard for comparison.
By xe2x80x9cbiological samplexe2x80x9d is intended any biological sample obtained from an individual, body fluid, cell line, tissue culture, or other source which contains the polypeptide of the present invention or mRNA. As indicated, biological samples include body fluids (such as semen, lymph, sera, plasma, urine, synovial fluid and spinal fluid) which contain the polypeptide of the present invention, and other tissue sources found to express the polypeptide of the present invention. Methods for obtaining tissue biopsies and body fluids from mammals are well known in the art. Where the biological sample is to include mRNA, a tissue biopsy is the preferred source.
The method(s) provided above may preferably be applied in a diagnostic method and/or kits in which polynucleotides and/or polypeptides are attached to a solid support. In one exemplary method, the support may be a xe2x80x9cgene chipxe2x80x9d or a xe2x80x9cbiological chipxe2x80x9d as described in U.S. Pat. Nos. 5,837,832, 5,874,219, and 5,856,174. Further, such a gene chip with polynucleotides of the present invention attached may be used to identify polymorphisms between the polynucleotide sequences, with polynucleotides isolated from a test subject. The knowledge of such polymorphisms (i.e. their location, as well as, their existence) would be beneficial in identifying disease loci for many disorders, including cancerous diseases and conditions. Such a method is described in U.S. Pat. Nos. 5,858,659 and 5,856,104. The U.S. Patents referenced supra are hereby incorporated by reference in their entirety herein.
The present invention encompasses polynucleotides of the present invention that are chemically synthesized, or reproduced as peptide nucleic acids (PNA), or according to other methods known in the art. The use of PNAs would serve as the preferred form if the polynucleotides are incorporated onto a solid support, or gene chip. For the purposes of the present invention, a peptide nucleic acid (PNA) is a polyamide type of DNA analog and the monomeric units for adenine, guanine, thymine and cytosine are available commercially (Perceptive Biosystems). Certain components of DNA, such as phosphorus, phosphorus oxides, or deoxyribose derivatives, are not present in PNAs. As disclosed by P. E. Nielsen, M. Egholm, R. H. Berg and O. Buchardt, Science 254, 1497 (1991); and M. Egholm, O. Buchardt, L. Christensen, C. Behrens, S. M. Freier, D. A. Driver, R. H. Berg, S. K. Kim, B. Norden, and P. E. Nielsen, Nature 365, 666 (1993), PNAs bind specifically and tightly to complementary DNA strands and are not degraded by nucleases. In fact, PNA binds more strongly to DNA than DNA itself does. This is probably because there is no electrostatic repulsion between the two strands, and also the polyamide backbone is more flexible. Because of this, PNA/DNA duplexes bind under a wider range of stringency conditions than DNA/DNA duplexes, making it easier to perform multiplex hybridization. Smaller probes can be used than with DNA due to the strong binding. In addition, it is more likely that single base mismatches can be determined with PNA/DNA hybridization because a single mismatch in a PNA/DNA 15-mer lowers the melting point (T.sub.m) by 8xc2x0-20xc2x0 C., vs. 4xc2x0-16xc2x0 C. for the DNA/DNA 15-mer duplex. Also, the absence of charge groups in PNA means that hybridization can be done at low ionic strengths and reduce possible interference by salt during the analysis.
The present invention is useful for detecting cancer in mammals. In particular the invention is useful during diagnosis of pathological cell proliferative neoplasias which include, but are not limited to: acute myelogenous leukemias including acute monocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute erythroleukemia, acute megakaryocytic leukemia, and acute undifferentiated leukemia, etc.; and chronic myelogenous leukemias including chronic myelomonocytic leukemia, chronic granulocytic leukemia, etc. Preferred mammals include monkeys, apes, cats, dogs, cows, pigs, horses, rabbits and humans. Particularly preferred are humans.
Pathological cell proliferative diseases, disorders, and/or conditions are often associated with inappropriate activation of proto-oncogenes. (Gelmann, E. P. et al., xe2x80x9cThe Etiology of Acute Leukemia: Molecular Genetics and Viral Oncology,xe2x80x9d in Neoplastic Diseases of the Blood, Vol 1., Wiernik, P. H. et al. eds., 161-182 (1985)). Neoplasias are now believed to result from the qualitative alteration of a normal cellular gene product, or from the quantitative modification of gene expression by insertion into the chromosome of a viral sequence, by chromosomal translocation of a gene to a more actively transcribed region, or by some other mechanism. (Gelmann et al., supra) It is likely that mutated or altered expression of specific genes is involved in the pathogenesis of some leukemias, among other tissues and cell types. (Gelmann et al., supra) Indeed, the human counterparts of the oncogenes involved in some animal neoplasias have been amplified or translocated in some cases of human leukemia and carcinoma. (Gelmann et al., supra) For example, c-myc expression is highly amplified in the non-lymphocytic leukemia cell line HL-60. When HL-60 cells are chemically induced to stop proliferation, the level of c-myc is found to be downregulated. (International Publication Number WO 91/15580) However, it has been shown that exposure of HL-60 cells to a DNA construct that is complementary to the 5xe2x80x2 end of c-myc or c-myb blocks translation of the corresponding mRNAs which downregulates expression of the c-myc or c-myb proteins and causes arrest of cell proliferation and differentiation of the treated cells. (International Publication Number WO 91/15580; Wickstrom et al., Proc. Natl. Acad. Sci. 85:1028 (1988); Anfossi et al., Proc. Natl. Acad. Sci. 86:3379 (1989)). However, the skilled artisan would appreciate the present invention""s usefulness would not be limited to treatment of proliferative diseases, disorders, and/or conditions of hematopoietic cells and tissues, in light of the numerous cells and cell types of varying origins which are known to exhibit proliferative phenotypes.
In addition to the foregoing, a polynucleotide can be used to control gene expression through triple helix formation or antisense DNA or RNA. Antisense techniques are discussed, for example, in Okano, J. Neurochem. 56: 560 (1991); xe2x80x9cOligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple helix formation is discussed in, for instance Lee et al., Nucleic Acids Research 6: 3073 (1979); Cooney et al., Science 241: 456 (1988); and Dervan et al., Science 251: 1360 (1991). Both methods rely on binding of the polynucleotide to a complementary DNA or RNA. For these techniques, preferred polynucleotides are usually oligonucleotides 20 to 40 bases in length and complementary to either the region of the gene involved in transcription (triple helixxe2x80x94see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense xe2x80x94Okano, J. Neurochem. 56:560 (1991); Oligodeoxy-nucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988).) Triple helix formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques are effective in model systems, and the information disclosed herein can be used to design antisense or triple helix polynucleotides in an effort to treat or prevent disease.
Polynucleotides of the present invention are also useful in gene therapy. One goal of gene therapy is to insert a normal gene into an organism having a defective gene, in an effort to correct the genetic defect. The polynucleotides disclosed in the present invention offer a means of targeting such genetic defects in a highly accurate manner. Another goal is to insert a new gene that was not present in the host genome, thereby producing a new trait in the host cell.
The polynucleotides are also useful for identifying individuals from minute biological samples. The United States military, for example, is considering the use of restriction fragment length polymorphism (RFLP) for identification of its personnel. In this technique, an individual""s genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identifying personnel. This method does not suffer from the current limitations of xe2x80x9cDog Tagsxe2x80x9d which can be lost, switched, or stolen, making positive identification difficult. The polynucleotides of the present invention can be used as additional DNA markers for RFLP.
The polynucleotides of the present invention can also be used as an alternative to RFLP, by determining the actual base-by-base DNA sequence of selected portions of an individual""s genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, individuals can be identified because each individual will have a unique set of DNA sequences. Once an unique ID database is established for an individual, positive identification of that individual, living or dead, can be made from extremely small tissue samples.
Forensic biology also benefits from using DNA-based identification techniques as disclosed herein. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, synovial fluid, amniotic fluid, breast milk, lymph, pulmonary sputum or surfactant, urine, fecal matter, etc., can be amplified using PCR. In one prior art technique, gene sequences amplified from polymorphic loci, such as DQa class II HLA gene, are used in forensic biology to identify individuals. (Erlich, H., PCR Technology, Freeman and Co. (1992).) Once these specific polymorphic loci are amplified, they are digested with one or more restriction enzymes, yielding an identifying set of bands on a Southern blot probed with DNA corresponding to the DQa class II HLA gene. Similarly, polynucleotides of the present invention can be used as polymorphic markers for forensic purposes.
There is also a need for reagents capable of identifying the source of a particular tissue. Such need arises, for example, in forensics when presented with tissue of unknown origin. Appropriate reagents can comprise, for example, DNA probes or primers specific to particular tissue prepared from the sequences of the present invention. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.
In the very least, the polynucleotides of the present invention can be used as molecular weight markers on Southern gels, as diagnostic probes for the presence of a specific mRNA in a particular cell type, as a probe to xe2x80x9csubtract-outxe2x80x9d known sequences in the process of discovering novel polynucleotides, for selecting and making oligomers for attachment to a xe2x80x9cgene chipxe2x80x9d or other support, to raise anti-DNA antibodies using DNA immunization techniques, and as an antigen to elicit an immune response.
Uses of the Polypeptides
Each of the polypeptides identified herein can be used in numerous ways. The following description should be considered exemplary and utilizes known techniques.
A polypeptide of the present invention can be used to assay protein levels in a biological sample using antibody-based techniques. For example, protein expression in tissues can be studied with classical immunohistological methods. (Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096 (1987).) Other antibody-based methods useful for detecting protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels are known in the art and include enzyme labels, such as, glucose oxidase, and radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99mTc), and fluorescent labels, such as fluorescein and rhodamine, and biotin.
In addition to assaying secreted protein levels in a biological sample, proteins can also be detected in vivo by imaging. Antibody labels or markers for in vivo imaging of protein include those detectable by X-radiography, NMR or ESR. For X-radiography, suitable labels include radioisotopes such as barium or cesium, which emit detectable radiation but are not overtly harmful to the subject. Suitable markers for NMR and ESR include those with a detectable characteristic spin, such as deuterium, which may be incorporated into the antibody by labeling of nutrients for the relevant hybridoma.
A protein-specific antibody or antibody fragment which has been labeled with an appropriate detectable imaging moiety, such as a radioisotope (for example, 131I, 112In, 99mTc), a radio-opaque substance, or a material detectable by nuclear magnetic resonance, is introduced (for example, parenterally, subcutaneously, or intraperitoneally) into the mammal. It will be understood in the art that the size of the subject and the imaging system used will determine the quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope moiety, for a human subject, the quantity of radioactivity injected will normally range from about 5 to 20 millicuries of 99 mTc. The labeled antibody or antibody fragment will then preferentially accumulate at the location of cells which contain the specific protein. In vivo tumor imaging is described in S. W. Burchiel et al., xe2x80x9cImmunopharmacokinetics of Radiolabeled Antibodies and Their Fragments.xe2x80x9d (Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, S. W. Burchiel and B. A. Rhodes, eds., Masson Publishing Inc. (1982).)
Thus, the invention provides a diagnostic method of a disorder, which involves (a) assaying the expression of a polypeptide of the present invention in cells or body fluid of an individual; (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of a disorder. With respect to cancer, the presence of a relatively high amount of transcript in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.
Moreover, polypeptides of the present invention can be used to treat, prevent, and/or diagnose disease. For example, patients can be administered a polypeptide of the present invention in an effort to replace absent or decreased levels of the polypeptide (e.g., insulin), to supplement absent or decreased levels of a different polypeptide (e.g., hemoglobin S for hemoglobin B, SOD, catalase, DNA repair proteins), to inhibit the activity of a polypeptide (e.g., an oncogene or tumor supressor), to activate the activity of a polypeptide (e.g., by binding to a receptor), to reduce the activity of a membrane bound receptor by competing with it for free ligand (e.g., soluble TNF receptors used in reducing inflammation), or to bring about a desired response (e.g., blood vessel growth inhibition, enhancement of the immune response to proliferative cells or tissues).
Similarly, antibodies directed to a polypeptide of the present invention can also be used to treat, prevent, and/or diagnose disease. For example, administration of an antibody directed to a polypeptide of the present invention can bind and reduce overproduction of the polypeptide. Similarly, administration of an antibody can activate the polypeptide, such as by binding to a polypeptide bound to a membrane (receptor).
At the very least, the polypeptides of the present invention can be used as molecular weight markers on SDS-PAGE gels or on molecular sieve gel filtration columns using methods well known to those of skill in the art. Polypeptides can also be used to raise antibodies, which in turn are used to measure protein expression from a recombinant cell, as a way of assessing transformation of the host cell. Moreover, the polypeptides of the present invention can be used to test the following biological activities.
Gene Therapy Methods
Another aspect of the present invention is to gene therapy methods for treating or preventing disorders, diseases and conditions. The gene therapy methods relate to the introduction of nucleic acid (DNA, RNA and antisense DNA or RNA) sequences into an animal to achieve expression of a polypeptide of the present invention. This method requires a polynucleotide which codes for a polypeptide of the invention that operatively linked to a promoter and any other genetic elements necessary for the expression of the polypeptide by the target tissue. Such gene therapy and delivery techniques are known in the art, see, for example, WO90/11092, which is herein incorporated by reference.
Thus, for example, cells from a patient may be engineered with a polynucleotide (DNA or RNA) comprising a promoter operably linked to a polynucleotide of the invention ex vivo, with the engineered cells then being provided to a patient to be treated with the polypeptide. Such methods are well-known in the art. For example, see Belldegrun et al., J. Natl. Cancer Inst., 85:207-216 (1993); Ferrantini et al., Cancer Research, 53:107-1112 (1993); Ferrantini et al., J. Immunology 153: 4604-4615 (1994); Kaido, T., et al., Int. J. Cancer 60: 221-229 (1995); Ogura et al., Cancer Research 50: 5102-5106 (1990); Santodonato, et al., Human Gene Therapy 7:1-10 (1996); Santodonato, et al., Gene Therapy 4:1246-1255 (1997); and Zhang, et al., Cancer Gene Therapy 3: 31-38 (1996)), which are herein incorporated by reference. In one embodiment, the cells which are engineered are arterial cells. The arterial cells may be reintroduced into the patient through direct injection to the artery, the tissues surrounding the artery, or through catheter injection.
As discussed in more detail below, the polynucleotide constructs can be delivered by any method that delivers injectable materials to the cells of an animal, such as, injection into the interstitial space of tissues (heart, muscle, skin, lung, liver, and the like). The polynucleotide constructs may be delivered in a pharmaceutically acceptable liquid or aqueous carrier.
In one embodiment, the polynucleotide of the invention is delivered as a naked polynucleotide. The term xe2x80x9cnakedxe2x80x9d polynucleotide, DNA or RNA refers to sequences that are free from any delivery vehicle that acts to assist, promote or facilitate entry into the cell, including viral sequences, viral particles, liposome formulations, lipofectin or precipitating agents and the like. However, the polynucleotides of the invention can also be delivered in liposome formulations and lipofectin formulations and the like can be prepared by methods well known to those skilled in the art. Such methods are described, for example, in U.S. Pat. Nos. 5,593,972, 5,589,466, and 5,580,859, which are herein incorporated by reference.
The polynucleotide vector constructs of the invention used in the gene therapy method are preferably constructs that will not integrate into the host genome nor will they contain sequences that allow for replication. Appropriate vectors include pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; pSVK3, pBPV, pMSG and pSVL available from Pharmacia; and pEF1/V5, pcDNA3.1, and pRc/CMV2 available from Invitrogen. Other suitable vectors will be readily apparent to the skilled artisan.
Any strong promoter known to those skilled in the art can be used for driving the expression of polynucleotide sequence of the invention. Suitable promoters include adenoviral promoters, such as the adenoviral major late promoter; or heterologous promoters, such as the cytomegalovirus (CMV) promoter; the respiratory syncytial virus (RSV) promoter; inducible promoters, such as the MMT promoter, the metallothionein promoter; heat shock promoters; the albumin promoter; the ApoAI promoter; human globin promoters; viral thymidine kinase promoters, such as the Herpes Simplex thymidine kinase promoter; retroviral LTRs; the b-actin promoter; and human growth hormone promoters. The promoter also may be the native promoter for the polynucleotides of the invention.
Unlike other gene therapy techniques, one major advantage of introducing naked nucleic acid sequences into target cells is the transitory nature of the polynucleotide synthesis in the cells. Studies have shown that non-replicating DNA sequences can be introduced into cells to provide production of the desired polypeptide for periods of up to six months.
The polynucleotide construct of the invention can be delivered to the interstitial space of tissues within the an animal, including of muscle, skin, brain, lung, liver, spleen, bone marrow, thymus, heart, lymph, blood, bone, cartilage, pancreas, kidney, gall bladder, stomach, intestine, testis, ovary, uterus, rectum, nervous system, eye, gland, and connective tissue. Interstitial space of the tissues comprises the intercellular, fluid, mucopolysaccharide matrix among the reticular fibers of organ tissues, elastic fibers in the walls of vessels or chambers, collagen fibers of fibrous tissues, or that same matrix within connective tissue ensheathing muscle cells or in the lacunae of bone. It is similarly the space occupied by the plasma of the circulation and the lymph fluid of the lymphatic channels. Delivery to the interstitial space of muscle tissue is preferred for the reasons discussed below. They may be conveniently delivered by injection into the tissues comprising these cells. They are preferably delivered to and expressed in persistent, non-dividing cells which are differentiated, although delivery and expression may be achieved in non-differentiated or less completely differentiated cells, such as, for example, stem cells of blood or skin fibroblasts. In vivo muscle cells are particularly competent in their ability to take up and express polynucleotides.
For the naked nucleic acid sequence injection, an effective dosage amount of DNA or RNA will be in the range of from about 0.05 mg/kg body weight to about 50 mg/kg body weight. Preferably the dosage will be from about 0.005 mg/kg to about 20 mg/kg and more preferably from about 0.05 mg/kg to about 5 mg/kg. Of course, as the artisan of ordinary skill will appreciate, this dosage will vary according to the tissue site of injection. The appropriate and effective dosage of nucleic acid sequence can readily be determined by those of ordinary skill in the art and may depend on the condition being treated and the route of administration.
The preferred route of administration is by the parenteral route of injection into the interstitial space of tissues. However, other parenteral routes may also be used, such as, inhalation of an aerosol formulation particularly for delivery to lungs or bronchial tissues, throat or mucous membranes of the nose. In addition, naked DNA constructs can be delivered to arteries during angioplasty by the catheter used in the procedure.
The naked polynucleotides are delivered by any method known in the art, including, but not limited to, direct needle injection at the delivery site, intravenous injection, topical administration, catheter infusion, and so-called xe2x80x9cgene gunsxe2x80x9d. These delivery methods are known in the art.
The constructs may also be delivered with delivery vehicles such as viral sequences, viral particles, liposome formulations, lipofectin, precipitating agents, etc. Such methods of delivery are known in the art.
In certain embodiments, the polynucleotide constructs of the invention are complexed in a liposome preparation. Liposomal preparations for use in the instant invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. However, cationic liposomes are particularly preferred because a tight charge complex can be formed between the cationic liposome and the polyanionic nucleic acid. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Felgner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7416 (1987), which is herein incorporated by reference); mRNA (Malone et al., Proc. Natl. Acad. Sci. USA, 86:6077-6081 (1989), which is herein incorporated by reference); and purified transcription factors (Debs et al., J. Biol. Chem., 265:10189-10192 (1990), which is herein incorporated by reference), in functional form.
Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes are particularly useful and are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Felgner et al., Proc. Natl Acad. Sci. USA, 84:7413-7416 (1987), which is herein incorporated by reference). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boehringer).
Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, e.g. PCT Publication NO: WO 90/11092 (which is herein incorporated by reference) for a description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes. Preparation of DOTMA liposomes is explained in the literature, see, e.g., Felgner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7417, which is herein incorporated by reference. Similar methods can be used to prepare liposomes from other cationic lipid materials.
Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl, choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.
For example, commercially dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), and dioleoylphosphatidyl ethanolamine (DOPE) can be used in various combinations to make conventional liposomes, with or without the addition of cholesterol. Thus, for example, DOPG/DOPC vesicles can be prepared by drying 50 mg each of DOPG and DOPC under a stream of nitrogen gas into a sonication vial. The sample is placed under a vacuum pump overnight and is hydrated the following day with deionized water. The sample is then sonicated for 2 hours in a capped vial, using a Heat Systems model 350 sonicator equipped with an inverted cup (bath type) probe at the maximum setting while the bath is circulated at 15EC. Alternatively, negatively charged vesicles can be prepared without sonication to produce multilamellar vesicles or by extrusion through nucleopore membranes to produce unilamellar vesicles of discrete size. Other methods are known and available to those of skill in the art.
The liposomes can comprise multilamellar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs), with SUVs being preferred. The various liposome-nucleic acid complexes are prepared using methods well known in the art. See, e.g., Straubinger et al., Methods of Immunology, 101:512-527 (1983), which is herein incorporated by reference. For example, MLVs containing nucleic acid can be prepared by depositing a thin film of phospholipid on the walls of a glass tube and subsequently hydrating with a solution of the material to be encapsulated. SUVs are prepared by extended sonication of MLVs to produce a homogeneous population of unilamellar liposomes. The material to be entrapped is added to a suspension of preformed MLVs and then sonicated. When using liposomes containing cationic lipids, the dried lipid film is resuspended in an appropriate solution such as sterile water or an isotonic buffer solution such as 10 mM Tris/NaCl, sonicated, and then the preformed liposomes are mixed directly with the DNA. The liposome and DNA form a very stable complex due to binding of the positively charged liposomes to the cationic DNA. SUVs find use with small nucleic acid fragments. LUVs are prepared by a number of methods, well known in the art. Commonly used methods include Ca2+-EDTA chelation (Papahadjopoulos et al., Biochim. Biophys. Acta, 394:483 (1975); Wilson et al., Cell, 17:77 (1979)); ether injection (Deamer et al., Biochim. Biophys. Acta, 443:629 (1976); Ostro et al., Biochem. Biophys. Res. Commun., 76:836 (1977); Fraley et al., Proc. Natl. Acad. Sci. USA, 76:3348 (1979)); detergent dialysis (Enoch et al., Proc. Natl. Acad. Sci. USA, 76:145 (1979)); and reverse-phase evaporation (REV) (Fraley et al., J. Biol. Chem., 255:10431 (1980); Szoka et al., Proc. Natl. Acad. Sci. USA, 75:145 (1978); Schaefer-Ridder et al., Science, 215:166 (1982)), which are herein incorporated by reference.
Generally, the ratio of DNA to liposomes will be from about 10:1 to about 1:10. Preferably, the ration will be from about 5:1 to about 1:5. More preferably, the ration will be about 3:1 to about 1:3. Still more preferably, the ratio will be about 1:1.
U.S. Pat. No. 5,676,954 (which is herein incorporated by reference) reports on the injection of genetic material, complexed with cationic liposomes carriers, into mice. U.S. Pat. Nos. 4,897,355, 4,946,787, 5,049,386, 5,459,127, 5,589,466, 5,693,622, 5,580,859, 5,703,055, and international publication NO: WO 94/9469 (which are herein incorporated by reference) provide cationic lipids for use in transfecting DNA into cells and mammals. U.S. Pat. Nos. 5,589,466, 5,693,622, 5,580,859, 5,703,055, and international publication NO: WO 94/9469 (which are herein incorporated by reference) provide methods for delivering DNA-cationic lipid complexes to mammals.
In certain embodiments, cells are engineered, ex vivo or in vivo, using a retroviral particle containing RNA which comprises a sequence encoding polypeptides of the invention. Retroviruses from which the retroviral plasmid vectors may be derived include, but are not limited to, Moloney Murine Leukemia Virus, spleen necrosis virus, Rous sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, gibbon ape leukemia virus, human immunodeficiency virus, Myeloproliferative Sarcoma Virus, and mammary tumor virus.
The retroviral plasmid vector is employed to transduce packaging cell lines to form producer cell lines. Examples of packaging cells which may be transfected include, but are not limited to, the PE501, PA317, R-2, R-AM, PA12, T19-14X, VT-19-17-H2, RCRE, RCRIP, GP+E-86, GP+envAm12, and DAN cell lines as described in Miller, Human Gene Therapy, 1:5-14 (1990), which is incorporated herein by reference in its entirety. The vector may transduce the packaging cells through any means known in the art. Such means include, but are not limited to, electroporation, the use of liposomes, and CaPO4 precipitation. In one alternative, the retroviral plasmid vector may be encapsulated into a liposome, or coupled to a lipid, and then administered to a host.
The producer cell line generates infectious retroviral vector particles which include polynucleotide encoding polypeptides of the invention. Such retroviral vector particles then may be employed, to transduce eukaryotic cells, either in vitro or in vivo. The transduced eukaryotic cells will express polypeptides of the invention.
In certain other embodiments, cells are engineered, ex vivo or in vivo, with polynucleotides of the invention contained in an adenovirus vector. Adenovirus can be manipulated such that it encodes and expresses polypeptides of the invention, and at the same time is inactivated in terms of its ability to replicate in a normal lytic viral life cycle. Adenovirus expression is achieved without integration of the viral DNA into the host cell chromosome, thereby alleviating concerns about insertional mutagenesis. Furthermore, adenoviruses have been used as live enteric vaccines for many years with an excellent safety profile (Schwartz et al., Am. Rev. Respir. Dis., 109:233-238 (1974)). Finally, adenovirus mediated gene transfer has been demonstrated in a number of instances including transfer of alpha-1-antitrypsin and CFTR to the lungs of cotton rats (Rosenfeld et al., Science, 252:431-434 (1991); Rosenfeld et al., Cell, 68:143-155 (1992)). Furthermore, extensive studies to attempt to establish adenovirus as a causative agent in human cancer were uniformly negative (Green et al. Proc. Natl. Acad. Sci. USA, 76:6606 (1979)).
Suitable adenoviral vectors useful in the present invention are described, for example, in Kozarsky and Wilson, Curr. Opin. Genet. Devel., 3:499-503 (1993); Rosenfeld et al., Cell, 68:143-155 (1992); Engelhardt et al., Human Genet. Ther., 4:759-769 (1993); Yang et al., Nature Genet., 7:362-369 (1994); Wilson et al., Nature, 365:691-692 (1993); and U.S. Pat. No. 5,652,224, which are herein incorporated by reference. For example, the adenovirus vector Ad2 is useful and can be grown in human 293 cells. These cells contain the E1 region of adenovirus and constitutively express E1a and E1b, which complement the defective adenoviruses by providing the products of the genes deleted from the vector. In addition to Ad2, other varieties of adenovirus (e.g., Ad3, Ad5, and Ad7) are also useful in the present invention.
Preferably, the adenoviruses used in the present invention are replication deficient. Replication deficient adenoviruses require the aid of a helper virus and/or packaging cell line to form infectious particles. The resulting virus is capable of infecting cells and can express a polynucleotide of interest which is operably linked to a promoter, but cannot replicate in most cells. Replication deficient adenoviruses may be deleted in one or more of all or a portion of the following genes: E1a, E1b, E3, E4, E2a, or L1 through L5.
In certain other embodiments, the cells are engineered, ex vivo or in vivo, using an adeno-associated virus (AAV). AAVs are naturally occurring defective viruses that require helper viruses to produce infectious particles (Muzyczka, Curr. Topics in Microbiol. Immunol., 158:97 (1992)). It is also one of the few viruses that may integrate its DNA into non-dividing cells. Vectors containing as little as 300 base pairs of AAV can be packaged and can integrate, but space for exogenous DNA is limited to about 4.5 kb. Methods for producing and using such AAVs are known in the art. See, for example, U.S. Pat. Nos. 5,139,941, 5,173,414, 5,354,678, 5,436,146, 5,474,935, 5,478,745, and 5,589,377.
For example, an appropriate AAV vector for use in the present invention will include all the sequences necessary for DNA replication, encapsidation, and host-cell integration. The polynucleotide construct containing polynucleotides of the invention is inserted into the AAV vector using standard cloning methods, such as those found in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press (1989). The recombinant AAV vector is then transfected into packaging cells which are infected with a helper virus, using any standard technique, including lipofection, electroporation, calcium phosphate precipitation, etc. Appropriate helper viruses include adenoviruses, cytomegaloviruses, vaccinia viruses, or herpes viruses. Once the packaging cells are transfected and infected, they will produce infectious AAV viral particles which contain the polynucleotide construct of the invention. These viral particles are then used to transduce eukaryotic cells, either ex vivo or in vivo. The transduced cells will contain the polynucleotide construct integrated into its genome, and will express the desired gene product.
Another method of gene therapy involves operably associating heterologous control regions and endogenous polynucleotide sequences (e.g. encoding the polypeptide sequence of interest) via homologous recombination (see, e.g., U.S. Pat. No. 5,641,670, issued Jun. 24, 1997; International Publication NO: WO 96/29411, published Sep. 26, 1996; International Publication NO: WO 94/12650, published Aug. 4, 1994; Koller et al., Proc. Natl. Acad. Sci. USA, 86:8932-8935 (1989); and Zijlstra et al., Nature, 342:435-438 (1989). This method involves the activation of a gene which is present in the target cells, but which is not normally expressed in the cells, or is expressed at a lower level than desired.
Polynucleotide constructs are made, using standard techniques known in the art, which contain the promoter with targeting sequences flanking the promoter. Suitable promoters are described herein. The targeting sequence is sufficiently complementary to an endogenous sequence to permit homologous recombination of the promoter-targeting sequence with the endogenous sequence. The targeting sequence will be sufficiently near the 5xe2x80x2 end of the desired endogenous polynucleotide sequence so the promoter will be operably linked to the endogenous sequence upon homologous recombination.
The promoter and the targeting sequences can be amplified using PCR. Preferably, the amplified promoter contains distinct restriction enzyme sites on the 5xe2x80x2 and 3xe2x80x2 ends. Preferably, the 3xe2x80x2 end of the first targeting sequence contains the same restriction enzyme site as the 5xe2x80x2 end of the amplified promoter and the 5xe2x80x2 end of the second targeting sequence contains the same restriction site as the 3xe2x80x2 end of the amplified promoter. The amplified promoter and targeting sequences are digested and ligated together.
The promoter-targeting sequence construct is delivered to the cells, either as naked polynucleotide, or in conjunction with transfection-facilitating agents, such as liposomes, viral sequences, viral particles, whole viruses, lipofection, precipitating agents, etc., described in more detail above. The P promoter-targeting sequence can be delivered by any method, included direct needle injection, intravenous injection, topical administration, catheter infusion, particle accelerators, etc. The methods are described in more detail below.
The promoter-targeting sequence construct is taken up by cells. Homologous recombination between the construct and the endogenous sequence takes place, such that an endogenous sequence is placed under the control of the promoter. The promoter then drives the expression of the endogenous sequence.
The polynucleotides encoding polypeptides of the present invention may be administered along with other polynucleotides encoding other angiongenic proteins. Angiogenic proteins include, but are not limited to, acidic and basic fibroblast growth factors, VEGF-1, VEGF-2 (VEGF-C), VEGF-3 (VEGF-B), epidermal growth factor alpha and beta, platelet-derived endothelial cell growth factor, platelet-derived growth factor, tumor necrosis factor alpha, hepatocyte growth factor, insulin like growth factor, colony stimulating factor, macrophage colony stimulating factor, granulocyte/macrophage colony stimulating factor, and nitric oxide synthase.
Preferably, the polynucleotide encoding a polypeptide of the invention contains a secretory signal sequence that facilitates secretion of the protein. Typically, the signal sequence is positioned in the coding region of the polynucleotide to be expressed towards or at the 5xe2x80x2 end of the coding region. The signal sequence may be homologous or heterologous to the polynucleotide of interest and may be homologous or heterologous to the cells to be transfected. Additionally, the signal sequence may be chemically synthesized using methods known in the art.
Any mode of administration of any of the above-described polynucleotides constructs can be used so long as the mode results in the expression of one or more molecules in an amount sufficient to provide a therapeutic effect. This includes direct needle injection, systemic injection, catheter infusion, biolistic injectors, particle accelerators (i.e., xe2x80x9cgene gunsxe2x80x9d), gelfoam sponge depots, other commercially available depot materials, osmotic pumps (e.g., Alza minipumps), oral or suppositorial solid (tablet or pill) pharmaceutical formulations, and decanting or topical applications during surgery. For example, direct injection of naked calcium phosphate-precipitated plasmid into rat liver and rat spleen or a protein-coated plasmid into the portal vein has resulted in gene expression of the foreign gene in the rat livers. (Kaneda et al., Science, 243:375 (1989)).
A preferred method of local administration is by direct injection. Preferably, a recombinant molecule of the present invention complexed with a delivery vehicle is administered by direct injection into or locally within the area of arteries. Administration of a composition locally within the area of arteries refers to injecting the composition centimeters and preferably, millimeters within arteries.
Another method of local administration is to contact a polynucleotide construct of the present invention in or around a surgical wound. For example, a patient can undergo surgery and the polynucleotide construct can be coated on the surface of tissue inside the wound or the construct can be injected into areas of tissue inside the wound.
Therapeutic compositions useful in systemic administration, include recombinant molecules of the present invention complexed to a targeted delivery vehicle of the present invention. Suitable delivery vehicles for use with systemic administration comprise liposomes comprising ligands for targeting the vehicle to a particular site.
Preferred methods of systemic administration, include intravenous injection, aerosol, oral and percutaneous (topical) delivery. Intravenous injections can be performed using methods standard in the art. Aerosol delivery can also be performed using methods standard in the art (see, for example, Stribling et al., Proc. Natl. Acad. Sci. USA, 189:11277-11281(1992), which is incorporated herein by reference). Oral delivery can be performed by complexing a polynucleotide construct of the present invention to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers, include plastic capsules or tablets, such as those known in the art. Topical delivery can be performed by mixing a polynucleotide construct of the present invention with a lipophilic reagent (e.g., DMSO) that is capable of passing into the skin.
Determining an effective amount of substance to be delivered can depend upon a number of factors including, for example, the chemical structure and biological activity of the substance, the age and weight of the animal, the precise condition requiring treatment and its severity, and the route of administration. The frequency of treatments depends upon a number of factors, such as the amount of polynucleotide constructs administered per dose, as well as the health and history of the subject. The precise amount, number of doses, and timing of doses will be determined by the attending physician or veterinarian. Therapeutic compositions of the present invention can be administered to any animal, preferably to mammals and birds. Preferred mammals include humans, dogs, cats, mice, rats, rabbits sheep, cattle, horses and pigs, with humans being particularly
Biological Activities
The polynucleotides or polypeptides, or agonists or antagonists of the present invention can be used in assays to test for one or more biological activities. If these polynucleotides and polypeptides do exhibit activity in a particular assay, it is likely that these molecules may be involved in the diseases associated with the biological activity. Thus, the polynucleotides or polypeptides, or agonists or antagonists could be used to treat the associated disease.
Immune Activity
Polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may be useful in treating, preventing, and/or diagnosing diseases, disorders, and/or conditions of the immune system, by, for example, activating or inhibiting the proliferation, differentiation, or mobilization (chemotaxis) of immune cells. Immune cells develop through a process called hematopoiesis, producing myeloid (platelets, red blood cells, neutrophils, and macrophages) and lymphoid (B and T lymphocytes) cells from pluripotent stem cells. The etiology of these immune diseases, disorders, and/or conditions may be genetic, somatic, such as cancer and some autoimmune diseases, acquired (e.g., by chemotherapy or toxins), or infectious. Moreover, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention can be used as a marker or detector of a particular immune system disease or disorder.
Polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may be useful in treating, preventing, and/or diagnosing diseases, disorders, and/or conditions of hematopoietic cells. Polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention could be used to increase differentiation and proliferation of hematopoietic cells, including the pluripotent stem cells, in an effort to treat or prevent those diseases, disorders, and/or conditions associated with a decrease in certain (or many) types hematopoietic cells. Examples of immunologic deficiency syndromes include, but are not limited to: blood protein diseases, disorders, and/or conditions (e.g., agammaglobulinemia, dysgammaglobulinemia), ataxia telangiectasia, common variable immunodeficiency, Digeorge Syndrome, HIV infection, HTLV-BLV infection, leukocyte adhesion deficiency syndrome, lymphopenia, phagocyte bactericidal dysfunction, severe combined immunodeficiency (SCIDs), Wiskott-Aldrich Disorder, anemia, thrombocytopenia, or hemoglobinuria.
Moreover, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention could also be used to modulate hemostatic (the stopping of bleeding) or thrombolytic activity (clot formation). For example, by increasing hemostatic or thrombolytic activity, polynucleotides or polypeptides, and/or agonists or antagonists of the present invention could be used to treat or prevent blood coagulation diseases, disorders, and/or conditions (e.g., afibrinogenemia, factor deficiencies), blood platelet diseases, disorders, and/or conditions (e.g., thrombocytopenia), or wounds resulting from trauma, surgery, or other causes. Alternatively, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention that can decrease hemostatic or thrombolytic activity could be used to inhibit or dissolve clotting. These molecules could be important in the treatment or prevention of heart attacks (infarction), strokes, or scarring.
The polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may be useful in treating, preventing, and/or diagnosing autoimmune disorders. Many autoimmune disorders result from inappropriate recognition of self as foreign material by immune cells. This inappropriate recognition results in an immune response leading to the destruction of the host tissue. Therefore, the administration of polynucleotides and polypeptides of the invention that can inhibit an immune response, particularly the proliferation, differentiation, or chemotaxis of T-cells, may be an effective therapy in preventing autoimmune disorders.
Autoimmune diseases or disorders that may be treated, prevented, and/or diagnosed by polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention include, but are not limited to, one or more of the following: autoimmune hemolytic anemia, autoimmune neonatal thrombocytopenia, idiopathic thrombocytopenia purpura, autoimmunocytopenia, hemolytic anemia, antiphospholipid syndrome, dermatitis, allergic encephalomyelitis, myocarditis, relapsing polychondritis, rheumatic heart disease, glomerulonephritis (e.g, IgA nephropathy), Multiple Sclerosis, Neuritis, Uveitis Ophthalmia, Polyendocrinopathies, Purpura (e.g., Henloch-Scoenlein purpura), Reiter""s Disease, Stiff-Man Syndrome, Autoimmune Pulmonary Inflammation, Autism, Guillain-Barre Syndrome, insulin dependent diabetes mellitis, and autoimmune inflammatory eye, autoimmune thyroiditis, hypothyroidism (i.e., Hashimoto""s thyroiditis, systemic lupus erhythematosus, Goodpasture""s syndrome, Pemphigus, Receptor autoimmunities such as, for example, (a) Graves"" Disease, (b) Myasthenia Gravis, and (c) insulin resistance, autoimmune hemolytic anemia, autoimmune thrombocytopenic purpura, rheumatoid arthritis, schleroderma with anti-collagen antibodies, mixed connective tissue disease, polymyositis/dermatomyositis, pernicious anemia, idiopathic Addison""s disease, infertility, glomerulonephritis such as primary glomerulonephritis and IgA nephropathy, bullous pemphigoid, Sjogren""s syndrome, diabetes millitus, and adrenergic drug resistance (including adrenergic drug resistance with asthma or cystic fibrosis), chronic active hepatitis, primary biliary cirrhosis, other endocrine gland failure, vitiligo, vasculitis, post-MI, cardiotomy syndrome, urticaria, atopic dermatitis, asthma, inflammatory myopathies, and other inflammatory, granulamatous, degenerative, and atrophic disorders.
Additional autoimmune disorders (that are probable) that may be treated, prevented, and/or diagnosed with the compositions of the invention include, but are not limited to, rheumatoid arthritis (often characterized, e.g., by immune complexes in joints), scleroderma with anti-collagen antibodies (often characterized, e.g., by nucleolar and other nuclear antibodies), mixed connective tissue disease (often characterized, e.g., by antibodies to extractable nuclear antigens (e.g., ribonucleoprotein)), polymyositis (often characterized, e.g., by nonhistone ANA), pernicious anemia (often characterized, e.g., by antiparietal cell, microsomes, and intrinsic factor antibodies), idiopathic Addison""s disease (often characterized, e.g., by humoral and cell-mediated adrenal cytotoxicity, infertility (often characterized, e.g., by antispermatozoal antibodies), glomerulonephritis (often characterized, e.g., by glomerular basement membrane antibodies or immune complexes), bullous pemphigoid (often characterized, e.g., by IgG and complement in basement membrane), Sjogren""s syndrome (often characterized, e.g., by multiple tissue antibodies, and/or a specific nonhistone ANA (SS-B)), diabetes millitus (often characterized, e.g., by cell-mediated and humoral islet cell antibodies), and adrenergic drug resistance (including adrenergic drug resistance with asthma or cystic fibrosis) (often characterized, e.g., by beta-adrenergic receptor antibodies).
Additional autoimmune disorders (that are possible) that may be treated, prevented, and/or diagnosed with the compositions of the invention include, but are not limited to, chronic active hepatitis (often characterized, e.g., by smooth muscle antibodies), primary biliary cirrhosis (often characterized, e.g., by mitchondrial antibodies), other endocrine gland failure (often characterized, e.g., by specific tissue antibodies in some cases), vitiligo (often characterized, e.g., by melanocyte antibodies), vasculitis (often characterized, e.g., by Ig and complement in vessel walls and/or low serum complement), post-MI (often characterized, e.g., by myocardial antibodies), cardiotomy syndrome (often characterized, e.g., by myocardial antibodies), urticaria (often characterized, e.g., by IgG and IgM antibodies to IgE), atopic dermatitis (often characterized, e.g., by IgG and IgM antibodies to IgE), asthma (often characterized, e.g., by IgG and IgM antibodies to IgE), and many other inflammatory, granulamatous, degenerative, and atrophic disorders.
In a preferred embodiment, the autoimmune diseases and disorders and/or conditions associated with the diseases and disorders recited above are treated, prevented, and/or diagnosed using for example, antagonists or agonists, polypeptides or polynucleotides, or antibodies of the present invention.
In a preferred embodiment polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention could be used as an agent to boost immunoresponsiveness among B cell and/or T cell immunodeficient individuals.
B cell immunodeficiencies that may be ameliorated or treated by administering the polypeptides or polynucleotides of the invention, and/or agonists thereof, include, but are not limited to, severe combined immunodeficiency (SCID)-X linked, SCID-autosomal, adenosine deaminase deficiency (ADA deficiency), X-linked agammaglobulinemia (XLA), Bruton""s disease, congenital agammaglobulinemia, X-linked infantile agammaglobulinemia, acquired agammaglobulinemia, adult onset agammaglobulinemia, late-onset agammaglobulinemia, dysgammaglobulinemia, hypogammaglobulinemia, transient hypogammaglobulinemia of infancy, unspecified hypogammaglobulinemia, agammaglobulinemia, common variable immunodeficiency (CVI) (acquired), Wiskott-Aldrich Syndrome (WAS), X-linked immunodeficiency with hyper IgM, non X-linked immunodeficiency with hyper IgM, selective IgA deficiency, IgG subclass deficiency (with or without IgA deficiency), antibody deficiency with normal or elevated Igs, immunodeficiency with thymoma, Ig heavy chain deletions, kappa chain deficiency, B cell lymphoproliferative disorder (BLPD), selective IgM immunodeficiency, recessive agammaglobulinemia (Swiss type), reticular dysgenesis, neonatal neutropenia, severe congenital leukopenia, thymic alymophoplasia-aplasia or dysplasia with immunodeficiency, ataxia-telangiectasia, short limbed dwarfism, X-linked lymphoproliferative syndrome (XLP), Nezelof syndrome-combined immunodeficiency with Igs, purine nucleoside phosphorylase deficiency (PNP), MHC Class II deficiency (Bare Lymphocyte Syndrome) and severe combined immunodeficiency.
T cell deficiencies that may be ameliorated or treated by administering the polypeptides or polynucleotides of the invention, and/or agonists thereof include, but are not limited to, for example, DiGeorge anomaly, thymic hypoplasia, third and fourth pharyngeal pouch syndrome, 22q 11.2 deletion, chronic mucocutaneous candidiasis, natural killer cell deficiency (NK), idiopathic CD4+ T-lymphocytopenia, immunodeficiency with predominant T cell defect (unspecified), and unspecified immunodeficiency of cell mediated immunity. In specific embodiments, DiGeorge anomaly or conditions associated with DiGeorge anomaly are ameliorated or treated by, for example, administering the polypeptides or polynucleotides of the invention, or antagonists or agonists thereof.
Other immunodeficiencies that may be ameliorated or treated by administering polypeptides or polynucleotides of the invention, and/or agonists thereof, include, but are not limited to, severe combined immunodeficiency (SCID; e.g., X-linked SCID, autosomal SCID, and adenosine deaminase deficiency), ataxia-telangiectasia, Wiskott-Aldrich syndrome, short-limber dwarfism, X-linked lymphoproliferative syndrome (XLP), Nezelof syndrome (e.g., purine nucleoside phosphorylase deficiency), MHC Class II deficiency. In specific embodiments, ataxia-telangiectasia or conditions associated with ataxia-telangiectasia are ameliorated or treated by administering the polypeptides or polynucleotides of the invention, and/or agonists thereof.
In a specific preferred embodiment, rheumatoid arthritis is treated, prevented, and/or diagnosed using polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention. In another specific preferred embodiment, systemic lupus erythemosus is treated, prevented, and/or diagnosed using polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention. In another specific preferred embodiment, idiopathic thrombocytopenia purpura is treated, prevented, and/or diagnosed using polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention. In another specific preferred embodiment IgA nephropathy is treated, prevented, and/or diagnosed using polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention. In a preferred embodiment, the autoimmune diseases and disorders and/or conditions associated with the diseases and disorders recited above are treated, prevented, and/or diagnosed using antibodies against the protein of the invention.
Similarly, allergic reactions and conditions, such as asthma (particularly allergic asthma) or other respiratory problems, may also be treated, prevented, and/or diagnosed using polypeptides, antibodies, or polynucleotides of the invention, and/or agonists or antagonists thereof. Moreover, these molecules can be used to treat, prevent, and/or diagnose anaphylaxis, hypersensitivity to an antigenic molecule, or blood group incompatibility.
Moreover, inflammatory conditions may also be treated, diagnosed, and/or prevented with polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention. Such inflammatory conditions include, but are not limited to, for example, respiratory disorders (such as, e.g., asthma and allergy); gastrointestinal disorders (such as, e.g., inflammatory bowel disease); cancers (such as, e.g., gastric, ovarian, lung, bladder, liver, and breast); CNS disorders (such as, e.g., multiple sclerosis, blood-brain barrier permeability, ischemic brain injury and/or stroke, traumatic brain injury, neurodegenerative disorders (such as, e.g., Parkinson""s disease and Alzheimer""s disease), AIDS-related dementia, and prion disease); cardiovascular disorders (such as, e.g., atherosclerosis, myocarditis, cardiovascular disease, and cardiopulmonary bypass complications); as well as many additional diseases, conditions, and disorders that are characterized by inflammation (such as, e.g., chronic hepatitis (B and C), rheumatoid arthritis, gout, trauma, septic shock, pancreatitis, sarcoidosis, dermatitis, renal ischemia-reperfusion injury, Grave""s disease, systemic lupus erythematosis, diabetes mellitus (i.e., type 1 diabetes), and allogenic transplant rejection).
In specific embodiments, polypeptides, antibodies, or polynucleotides of the invention, and/or agonists or antagonists thereof, are useful to treat, diagnose, and/or prevent transplantation rejections, graft-versus-host disease, autoimmune and inflammatory diseases (e.g., immune complex-induced vasculitis, glomerulonephritis, hemolytic anemia, myasthenia gravis, type II collagen-induced arthritis, experimental allergic and hyperacute xenograft rejection, rheumatoid arthritis, and systemic lupus erythematosus (SLE). Organ rejection occurs by host immune cell destruction of the transplanted tissue through an immune response. Similarly, an immune response is also involved in GVHD, but, in this case, the foreign transplanted immune cells destroy the host tissues. Polypeptides, antibodies, or polynucleotides of the invention, and/or agonists or antagonists thereof, that inhibit an immune response, particularly the activation, proliferation, differentiation, or chemotaxis of T-cells, may be an effective therapy in preventing organ rejection or GVHD.
Similarly, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may also be used to modulate and/or diagnose inflammation. For example, since polypeptides, antibodies, or polynucleotides of the invention, and/or agonists or antagonists of the invention may inhibit the activation, proliferation and/or differentiation of cells involved in an inflammatory response, these molecules can be used to treat, diagnose, or prognose, inflammatory conditions, both chronic and acute conditions, including, but not limited to, inflammation associated with infection (e.g., septic shock, sepsis, or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine induced lung injury, inflammatory bowel disease, Crohn""s disease, and resulting from over production of cytokines (e.g., TNF or IL-1.).
Polypeptides, antibodies, polynucleotides and/or agonists or antagonists of the invention can be used to treat, detect, and/or prevent infectious agents. For example, by increasing the immune response, particularly increasing the proliferation activation and/or differentiation of B and/or T cells, infectious diseases may be treated, detected, and/or prevented. The immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may also directly inhibit the infectious agent (refer to section of application listing infectious agents, etc), without necessarily eliciting an immune response.
Additional preferred embodiments of the invention include, but are not limited to, the use of polypeptides, antibodies, polynucleotides and/or agonists or antagonists in the following applications:
Administration to an animal (e.g., mouse, rat, rabbit, hamster, guinea pig, pigs, micro-pig, chicken, camel, goat, horse, cow, sheep, dog, cat, non-human primate, and human, most preferably human) to boost the immune system to produce increased quantities of one or more antibodies (e.g., IgG, IgA, IgM, and IgE), to induce higher affinity antibody production (e.g., IgG, IgA, IgM, and IgE), and/or to increase an immune response.
Administration to an animal (including, but not limited to, those listed above, and also including transgenic animals) incapable of producing functional endogenous antibody molecules or having an otherwise compromised endogenous immune system, but which is capable of producing human immunoglobulin molecules by means of a reconstituted or partially reconstituted immune system from another animal (see, e.g., published PCT Application Nos. WO98/24893, WO/9634096, WO/9633735, and WO/9110741.
A vaccine adjuvant that enhances immune responsiveness to specific antigen.
An adjuvant to enhance tumor-specific immune responses.
An adjuvant to enhance anti-viral immune responses. Anti-viral immune responses that may be enhanced using the compositions of the invention as an adjuvant, include virus and virus associated diseases or symptoms described herein or otherwise known in the art. In specific embodiments, the compositions of the invention are used as an adjuvant to enhance an immune response to a virus, disease, or symptom selected from the group consisting of: AIDS, meningitis, Dengue, EBV, and hepatitis (e.g., hepatitis B). In another specific embodiment, the compositions of the invention are used as an adjuvant to enhance an immune response to a virus, disease, or symptom selected from the group consisting of: HIV/AIDS, Respiratory syncytial virus, Dengue, Rotavirus, Japanese B encephalitis, Influenza A and B, Parainfluenza, Measles, Cytomegalovirus, Rabies, Junin, Chikungunya, Rift Valley fever, Herpes simplex, and yellow fever.
An adjuvant to enhance anti-bacterial or anti-fungal immune responses. Anti-bacterial or anti-fungal immune responses that may be enhanced using the compositions of the invention as an adjuvant, include bacteria or fungus and bacteria or fungus associated diseases or symptoms described herein or otherwise known in the art. In specific embodiments, the compositions of the invention are used as an adjuvant to enhance an immune response to a bacteria or fungus, disease, or symptom selected from the group consisting of: tetanus, Diphtheria, botulism, and meningitis type B. In another specific embodiment, the compositions of the invention are used as an adjuvant to enhance an immune response to a bacteria or fungus, disease, or symptom selected from the group consisting of: Vibrio cholerae, Mycobacterium leprae, Salmonella typhi, Salmonella paratyphi, Meisseria meningitidis, Streptococcus pneumoniae, Group B streptococcus, Shigella spp., Enterotoxigenic Escherichia coli, Enterohemorrhagic E. coli, Borrelia burgdorferi, and Plasmodium (malaria).
An adjuvant to enhance anti-parasitic immune responses. Anti-parasitic immune responses that may be enhanced using the compositions of the invention as an adjuvant, include parasite and parasite associated diseases or symptoms described herein or otherwise known in the art. In specific embodiments, the compositions of the invention are used as an adjuvant to enhance an immune response to a parasite. In another specific embodiment, the compositions of the invention are used as an adjuvant to enhance an immune response to Plasmodium (malaria).
As a stimulator of B cell responsiveness to pathogens.
As an activator of T cells.
As an agent that elevates the immune status of an individual prior to their receipt of immunosuppressive therapies.
As an agent to induce higher affinity antibodies.
As an agent to increase serum immunoglobulin concentrations.
As an agent to accelerate recovery of immunocompromised individuals.
As an agent to boost immunoresponsiveness among aged populations.
As an immune system enhancer prior to, during, or after bone marrow transplant and/or other transplants (e.g., allogeneic or xenogeneic organ transplantation). With respect to transplantation, compositions of the invention may be administered prior to, concomitant with, and/or after transplantation. In a specific embodiment, compositions of the invention are administered after transplantation, prior to the beginning of recovery of T-cell populations. In another specific embodiment, compositions of the invention are first administered after transplantation after the beginning of recovery of T cell populations, but prior to full recovery of B cell populations.
As an agent to boost immunoresponsiveness among individuals having an acquired loss of B cell function. Conditions resulting in an acquired loss of B cell function that may be ameliorated or treated by administering the polypeptides, antibodies, polynucleotides and/or agonists or antagonists thereof, include, but are not limited to, HIV Infection, AIDS, bone marrow transplant, and B cell chronic lymphocytic leukemia (CLL).
As an agent to boost immunoresponsiveness among individuals having a temporary immune deficiency. Conditions resulting in a temporary immune deficiency that may be ameliorated or treated by administering the polypeptides, antibodies, polynucleotides and/or agonists or antagonists thereof, include, but are not limited to, recovery from viral infections (e.g., influenza), conditions associated with malnutrition, recovery from infectious mononucleosis, or conditions associated with stress, recovery from measles, recovery from blood transfusion, recovery from surgery.
As a regulator of antigen presentation by monocytes, dendritic cells, and/or B-cells. In one embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention enhance antigen presentation or antagonizes antigen presentation in vitro or in vivo. Moreover, in related embodiments, said enhancement or antagonization of antigen presentation may be useful as an anti-tumor treatment or to modulate the immune system.
As an agent to direct an individuals immune system towards development of a humoral response (i.e. TH2) as opposed to a TH1 cellular response.
As a means to induce tumor proliferation and thus make it more susceptible to anti-neoplastic agents. For example, multiple myeloma is a slowly dividing disease and is thus refractory to virtually all anti-neoplastic regimens. If these cells were forced to proliferate more rapidly their susceptibility profile would likely change.
As a stimulator of B cell production in pathologies such as AIDS, chronic lymphocyte disorder and/or Common Variable Immunodificiency.
As a therapy for generation and/or regeneration of lymphoid tissues following surgery, trauma or genetic defect.
As a gene-based therapy for genetically inherited disorders resulting in immuno-incompetence such as observed among SCID patients.
As an antigen for the generation of antibodies to inhibit or enhance immune mediated responses against polypeptides of the invention.
As a means of activating T cells.
As a means of activating monocytes/macrophages to defend against parasitic diseases that effect monocytes such as Leshmania.
As pretreatment of bone marrow samples prior to transplant. Such treatment would increase B cell representation and thus accelerate recover.
As a means of regulating secreted cytokines that are elicited by polypeptides of the invention.
Additionally, polypeptides or polynucleotides of the invention, and/or agonists thereof, may be used to treat or prevent IgE-mediated allergic reactions. Such allergic reactions include, but are not limited to, asthma, rhinitis, and eczema.
All of the above described applications as they may apply to veterinary medicine.
Antagonists of the invention include, for example, binding and/or inhibitory antibodies, antisense nucleic acids, or ribozymes. These would be expected to reverse many of the activities of the ligand described above as well as find clinical or practical application as:
A means of blocking various aspects of immune responses to foreign agents or self. Examples include autoimmune disorders such as lupus, and arthritis, as well as immunoresponsiveness to skin allergies, inflammation, bowel disease, injury and pathogens.
A therapy for preventing the B cell proliferation and Ig secretion associated with autoimmune diseases such as idiopathic thrombocytopenic purpura, systemic lupus erythramatosus and MS.
An inhibitor of B and/or T cell migration in endothelial cells. This activity disrupts tissue architecture or cognate responses and is useful, for example in disrupting immune responses, and blocking sepsis.
An inhibitor of graft versus host disease or transplant rejection.
A therapy for B cell and/or T cell malignancies such as ALL, Hodgkins disease, non-Hodgkins lymphoma, Chronic lymphocyte leukemia, plasmacytomas, multiple myeloma, Burkitt""s lymphoma, and EBV-transformed diseases.
A therapy for chronic hypergammaglobulinemeia evident in such diseases as monoclonalgammopathy of undetermined significance (MGUS), Waldenstrom""s disease, related idiopathic monoclonalgammopathies, and plasmacytomas.
A therapy for decreasing cellular proliferation of Large B-cell Lymphomas.
A means of decreasing the involvement of B cells and Ig associated with Chronic Myelogenous Leukemia.
An immunosuppressive agent(s).
Polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may be used to modulate IgE concentrations in vitro or in vivo.
In another embodiment, administration of polypeptides, antibodies, polynucleotides and/or agonists or antagonists of the invention, may be used to treat or prevent IgE-mediated allergic reactions including, but not limited to, asthma, rhinitis, and eczema.
The agonists and antagonists may be employed in a composition with a pharmaceutically acceptable carrier, e.g., as described herein.
The agonists or antagonists may be employed for instance to inhibit polypeptide chemotaxis and activation of macrophages and their precursors, and of neutrophils, basophils, B lymphocytes and some T-cell subsets, e.g., activated and CD8 cytotoxic T cells and natural killer cells, in certain auto-immune and chronic inflammatory and infective diseases. Examples of autoimmune diseases are described herein and include multiple sclerosis, and insulin-dependent diabetes. The antagonists or agonists may also be employed to treat infectious diseases including silicosis, sarcoidosis, idiopathic pulmonary fibrosis by, for example, preventing the recruitment and activation of mononuclear phagocytes. They may also be employed to treat idiopathic hyper-eosinophilic syndrome by, for example, preventing eosinophil production and migration. The antagonists or agonists or may also be employed for treating atherosclerosis, for example, by preventing monocyte infiltration in the artery wall.
Antibodies against polypeptides of the invention may be employed to treat ARDS.
Agonists and/or antagonists of the invention also have uses in stimulating wound and tissue repair, stimulating angiogenesis, stimulating the repair of vascular or lymphatic diseases or disorders. Additionally, agonists and antagonists of the invention may be used to stimulate the regeneration of mucosal surfaces.
In a specific embodiment, polynucleotides or polypeptides, and/or agonists thereof are used to treat or prevent a disorder characterized by primary or acquired immunodeficiency, deficient serum immunoglobulin production, recurrent infections, and/or immune system dysfunction. Moreover, polynucleotides or polypeptides, and/or agonists thereof may be used to treat or prevent infections of the joints, bones, skin, and/or parotid glands, blood-borne infections (e.g., sepsis, meningitis, septic arthritis, and/or osteomyelitis), autoimmune diseases (e.g., those disclosed herein), inflammatory disorders, and malignancies, and/or any disease or disorder or condition associated with these infections, diseases, disorders and/or malignancies) including, but not limited to, CVID, other primary immune deficiencies, HIV disease, CLL, recurrent bronchitis, sinusitis, otitis media, conjunctivitis, pneumonia, hepatitis, meningitis, herpes zoster (e.g., severe herpes zoster), and/or pneumocystis carnii.
In another embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention are used to treat, and/or diagnose an individual having common variable immunodeficiency disease (xe2x80x9cCVIDxe2x80x9d; also known as xe2x80x9cacquired agammaglobulinemiaxe2x80x9d and xe2x80x9cacquired hypogammaglobulinemiaxe2x80x9d) or a subset of this disease.
In a specific embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention may be used to treat, diagnose, and/or prevent (1) cancers or neoplasms and (2) autoimmune cell or tissue-related cancers or neoplasms. In a preferred embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention conjugated to a toxin or a radioactive isotope, as described herein, may be used to treat, diagnose, and/or prevent acute myelogeneous leukemia. In a further preferred embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of the present invention conjugated to a toxin or a radioactive isotope, as described herein, may be used to treat, diagnose, and/or prevent, chronic myelogeneous leukemia, multiple myeloma, non-Hodgkins lymphoma, and/or Hodgkins disease.
In another specific embodiment, polynucleotides or polypeptides, and/or agonists or antagonists of the invention may be used to treat, diagnose, prognose, and/or prevent selective IgA deficiency, myeloperoxidase deficiency, C2 deficiency, ataxia-telangiectasia, DiGeorge anomaly, common variable immunodeficiency (CVI), X-linked agammaglobulinemia, severe combined immunodeficiency (SCID), chronic granulomatous disease (CGD), and Wiskott-Aldrich syndrome.
Examples of autoimmune disorders that can be treated or detected are described above and also include, but are not limited to: Addison""s Disease, hemolytic anemia, antiphospholipid syndrome, rheumatoid arthritis, dermatitis, allergic encephalomyelitis, glomerulonephritis, Goodpasture""s Syndrome, Graves"" Disease, Multiple Sclerosis, Myasthenia Gravis, Neuritis, Ophthalmia, Bullous Pemphigoid, Pemphigus, Polyendocrinopathies, Purpura, Reiter""s Disease, Stiff-Man Syndrome, Autoimmune Thyroiditis, Systemic Lupus Erythematosus, Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulin dependent diabetes mellitis, and autoimmune inflammatory eye disease.
In a preferred embodiment, the autoimmune diseases and disorders and/or conditions associated with the diseases and disorders recited above are treated, prognosed, prevented, and/or diagnosed using antibodies against the polypeptide of the invention.
As an agent to boost immunoresponsiveness among B cell immunodeficient individuals, such as, for example, an individual who has undergone a partial or complete splenectomy.
Additionally, polynucleotides, polypeptides, and/or antagonists of the invention may affect apoptosis, and therefore, would be useful in treating a number of diseases associated with increased cell survival or the inhibition of apoptosis. For example, diseases associated with increased cell survival or the inhibition of apoptosis that could be treated or detected by polynucleotides, polypeptides, and/or antagonists of the invention, include cancers (such as follicular lymphomas, carcinomas with p53 mutations, and hormone-dependent tumors, including, but not limited to colon cancer, cardiac tumors, pancreatic cancer, melanoma, retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicular cancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma, endothelioma, osteoblastoma, osteoclastoma, osteosarcoma, chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi""s sarcoma and ovarian cancer); autoimmune disorders (such as, multiple sclerosis, Sjogren""s syndrome, Hashimoto""s thyroiditis, biliary cirrhosis, Behcet""s disease, Crohn""s disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) and viral infections (such as herpes viruses, pox viruses and adenoviruses), inflammation, graft v. host disease, acute graft rejection, and chronic graft rejection. In preferred embodiments, polynucleotides, polypeptides, and/or antagonists of the invention are used to inhibit growth, progression, and/or metastisis of cancers, in particular those listed above.
Additional diseases or conditions associated with increased cell survival that could be treated or detected by polynucleotides, polypeptides, and/or antagonists of the invention, include, but are not limited to, progression, and/or metastases of malignancies and related disorders such as leukemia (including acute leukemias (e.g., acute lymphocytic leukemia, acute myelocytic leukemia (including myeloblastic, promyelocytic, myelomonocytic, monocytic, and erythroleukemia)) and chronic leukemias (e.g., chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia)), polycythemia vera, lymphomas (e.g., Hodgkin""s disease and non-Hodgkin""s disease), multiple myeloma, Waldenstrom""s macroglobulinemia, heavy chain disease, and solid tumors including, but not limited to, sarcomas and carcinomas such as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing""s tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm""s tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, and retinoblastoma.
Diseases associated with increased apoptosis that could be treated or detected by polynucleotides, polypeptides, and/or antagonists of the invention, include AIDS; neurodegenerative disorders (such as Alzheimer""s disease, Parkinson""s disease, Amyotrophic lateral sclerosis, Retinitis pigmentosa, Cerebellar degeneration and brain tumor or prior associated disease); autoimmune disorders (such as, multiple sclerosis, Sjogren""s syndrome, Hashimoto""s thyroiditis, biliary cirrhosis, Behcet""s disease, Crohn""s disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) myelodysplastic syndromes (such as aplastic anemia), graft v. host disease, ischemic injury (such as that caused by myocardial infarction, stroke and reperfusion injury), liver injury (e.g., hepatitis related liver injury, ischemia/reperfusion injury, cholestosis (bile duct injury) and liver cancer); toxin-induced liver disease (such as that caused by alcohol), septic shock, cachexia and anorexia.
Hyperproliferative diseases and/or disorders that could be detected and/or treated by polynucleotides, polypeptides, and/or antagonists of the invention, include, but are not limited to neoplasms located in the: liver, abdomen, bone, breast, digestive system, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, and urogenital.
Similarly, other hyperproliferative disorders can also be treated or detected by polynucleotides, polypeptides, and/or antagonists of the invention. Examples of such hyperproliferative disorders include, but are not limited to: hypergammaglobulinemia, lymphoproliferative disorders, paraproteinemias, purpura, sarcoidosis, Sezary Syndrome, Waldenstron""s Macroglobulinemia, Gaucher""s Disease, histiocytosis, and any other hyperproliferative disease, besides neoplasia, located in an organ system listed above.
Hyperproliferative Disorders
A polynucleotides or polypeptides, or agonists or antagonists of the invention can be used to treat, prevent, and/or diagnose hyperproliferative diseases, disorders, and/or conditions, including neoplasms. A polynucleotides or polypeptides, or agonists or antagonists of the present invention may inhibit the proliferation of the disorder through direct or indirect interactions. Alternatively, a polynucleotides or polypeptides, or agonists or antagonists of the present invention may proliferate other cells which can inhibit the hyperproliferative disorder.
For example, by increasing an immune response, particularly increasing antigenic qualities of the hyperproliferative disorder or by proliferating, differentiating, or mobilizing T-cells, hyperproliferative diseases, disorders, and/or conditions can be treated, prevented, and/or diagnosed. This immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, decreasing an immune response may also be a method of treating, preventing, and/or diagnosing hyperproliferative diseases, disorders, and/or conditions, such as a chemotherapeutic agent.
Examples of hyperproliferative diseases, disorders, and/or conditions that can be treated, prevented, and/or diagnosed by polynucleotides or polypeptides, or agonists or antagonists of the present invention include, but are not limited to neoplasms located in the: colon, abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, and urogenital.
Similarly, other hyperproliferative diseases, disorders, and/or conditions can also be treated, prevented, and/or diagnosed by a polynucleotides or polypeptides, or agonists or antagonists of the present invention. Examples of such hyperproliferative diseases, disorders, and/or conditions include, but are not limited to: hypergammaglobulinemia, lymphoproliferative diseases, disorders, and/or conditions, paraproteinemias, purpura, sarcoidosis, Sezary Syndrome, Waldenstron""s Macroglobulinemia, Gaucher""s Disease, histiocytosis, and any other hyperproliferative disease, besides neoplasia, located in an organ system listed above.
One preferred embodiment utilizes polynucleotides of the present invention to inhibit aberrant cellular division, by gene therapy using the present invention, and/or protein fusions or fragments thereof.
Thus, the present invention provides a method for treating or preventing cell proliferative diseases, disorders, and/or conditions by inserting into an abnormally proliferating cell a polynucleotide of the present invention, wherein said polynucleotide represses said expression.
Another embodiment of the present invention provides a method of treating or preventing cell-proliferative diseases, disorders, and/or conditions in individuals comprising administration of one or more active gene copies of the present invention to an abnormally proliferating cell or cells. In a preferred embodiment, polynucleotides of the present invention is a DNA construct comprising a recombinant expression vector effective in expressing a DNA sequence encoding said polynucleotides. In another preferred embodiment of the present invention, the DNA construct encoding the poynucleotides of the present invention is inserted into cells to be treated utilizing a retrovirus, or more preferably an adenoviral vector (See G J. Nabel, et. al., PNAS1999 96: 324-326, which is hereby incorporated by reference). In a most preferred embodiment, the viral vector is defective and will not transform non-proliferating cells, only proliferating cells. Moreover, in a preferred embodiment, the polynucleotides of the present invention inserted into proliferating cells either alone, or in combination with or fused to other polynucleotides, can then be modulated via an external stimulus (i.e. magnetic, specific small molecule, chemical, or drug administration, etc.), which acts upon the promoter upstream of said polynucleotides to induce expression of the encoded protein product. As such the beneficial therapeutic affect of the present invention may be expressly modulated (i.e. to increase, decrease, or inhibit expression of the present invention) based upon said external stimulus.
Polynucleotides of the present invention may be useful in repressing expression of oncogenic genes or antigens. By xe2x80x9crepressing expression of the oncogenic genesxe2x80x9d is intended the suppression of the transcription of the gene, the degradation of the gene transcript (pre-message RNA), the inhibition of splicing, the destruction of the messenger RNA, the prevention of the post-translational modifications of the protein, the destruction of the protein, or the inhibition of the normal function of the protein.
For local administration to abnormally proliferating cells, polynucleotides of the present invention may be administered by any method known to those of skill in the art including, but not limited to transfection, electroporation, microinjection of cells, or in vehicles such as liposomes, lipofectin, or as naked polynucleotides, or any other method described throughout the specification. The polynucleotide of the present invention may be delivered by known gene delivery systems such as, but not limited to, retroviral vectors (Gilboa, J. Virology 44:845 (1982); Hocke, Nature 320:275 (1986); Wilson, et al., Proc. Natl. Acad. Sci. U.S.A. 85:3014), vaccinia virus system (Chakrabarty et al., Mol. Cell Biol. 5:3403 (1985) or other efficient DNA delivery systems (Yates et al., Nature 313:812 (1985)) known to those skilled in the art. These references are exemplary only and are hereby incorporated by reference. In order to specifically deliver or transfect cells which are abnormally proliferating and spare non-dividing cells, it is preferable to utilize a retrovirus, or adenoviral (as described in the art and elsewhere herein) delivery system known to those of skill in the art. Since host DNA replication is required for retroviral DNA to integrate and the retrovirus will be unable to self replicate due to the lack of the retrovirus genes needed for its life cycle. Utilizing such a retroviral delivery system for polynucleotides of the present invention will target said gene and constructs to abnormally proliferating cells and will spare the non-dividing normal cells.
The polynucleotides of the present invention may be delivered directly to cell proliferative disorder/disease sites in internal organs, body cavities and the like by use of imaging devices used to guide an injecting needle directly to the disease site. The polynucleotides of the present invention may also be administered to disease sites at the time of surgical intervention.
By xe2x80x9ccell proliferative diseasexe2x80x9d is meant any human or animal disease or disorder, affecting any one or any combination of organs, cavities, or body parts, which is characterized by single or multiple local abnormal proliferations of cells, groups of cells, or tissues, whether benign or malignant.
Any amount of the polynucleotides of the present invention may be administered as long as it has a biologically inhibiting effect on the proliferation of the treated cells. Moreover, it is possible to administer more than one of the polynucleotide of the present invention simultaneously to the same site. By xe2x80x9cbiologically inhibitingxe2x80x9d is meant partial or total growth inhibition as well as decreases in the rate of proliferation or growth of the cells. The biologically inhibitory dose may be determined by assessing the effects of the polynucleotides of the present invention on target malignant or abnormally proliferating cell growth in tissue culture, tumor growth in animals and cell cultures, or any other method known to one of ordinary skill in the art.
The present invention is further directed to antibody-based therapies which involve administering of anti-polypeptides and anti-polynucleotide antibodies to a mammalian, preferably human, patient for treating, preventing, and/or diagnosing one or more of the described diseases, disorders, and/or conditions. Methods for producing anti-polypeptides and anti-polynucleotide antibodies polyclonal and monoclonal antibodies are described in detail elsewhere herein. Such antibodies may be provided in pharmaceutically acceptable compositions as known in the art or as described herein.
A summary of the ways in which the antibodies of the present invention may be used therapeutically includes binding polynucleotides or polypeptides of the present invention locally or systemically in the body or by direct cytotoxicity of the antibody, e.g. as mediated by complement (CDC) or by effector cells (ADCC). Some of these approaches are described in more detail below. Armed with the teachings provided herein, one of ordinary skill in the art will know how to use the antibodies of the present invention for diagnostic, monitoring or therapeutic purposes without undue experimentation.
In particular, the antibodies, fragments and derivatives of the present invention are useful for treating, preventing, and/or diagnosing a subject having or developing cell proliferative and/or differentiation diseases, disorders, and/or conditions as described herein. Such treatment comprises administering a single or multiple doses of the antibody, or a fragment, derivative, or a conjugate thereof.
The antibodies of this invention may be advantageously utilized in combination with other monoclonal or chimeric antibodies, or with lymphokines or hematopoietic growth factors, for example, which serve to increase the number or activity of effector cells which interact with the antibodies.
It is preferred to use high affinity and/or potent in vivo inhibiting and/or neutralizing antibodies against polypeptides or polynucleotides of the present invention, fragments or regions thereof, for both immunoassays directed to and therapy of diseases, disorders, and/or conditions related to polynucleotides or polypeptides, including fragments thereof, of the present invention. Such antibodies, fragments, or regions, will preferably have an affinity for polynucleotides or polypeptides, including fragments thereof. Preferred binding affinities include those with a dissociation constant or Kd less than 5xc3x9710xe2x88x926 M, 10xe2x88x926 M, 5xc3x9710xe2x88x927 M, 10xe2x88x927 M, 5xc3x9710xe2x88x928 M 10xe2x88x928 M, 5xc3x9710xe2x88x929 M, 10xe2x88x929 M, 5xc3x9710xe2x88x9210 M, 10xe2x88x9210 M, 5xc3x9710xe2x88x9211 M, 10xe2x88x9211 M, 5xc3x9710xe2x88x9212 M, 10xe2x88x9212 M, 5xc3x9710xe2x88x9213 M, 10xe2x88x9213 M, 5xc3x9710xe2x88x9214 M, 10xe2x88x9214 M, 5xc3x9710xe2x88x9215 M, and 10xe2x88x9215 M.
Moreover, polypeptides of the present invention are useful in inhibiting the angiogenesis of proliferative cells or tissues, either alone, as a protein fusion, or in combination with other polypeptides directly or indirectly, as described elsewhere herein. In a most preferred embodiment, said anti-angiogenesis effect may be achieved indirectly, for example, through the inhibition of hematopoietic, tumor-specific cells, such as tumor-associated macrophages (See Joseph I B, et al. J Natl Cancer Inst, 90(21):1648-53 (1998), which is hereby incorporated by reference). Antibodies directed to polypeptides or polynucleotides of the present invention may also result in inhibition of angiogenesis directly, or indirectly (See Witte L, et al., Cancer Metastasis Rev. 17(2):155-61 (1998), which is hereby incorporated by reference)).
Polypeptides, including protein fusions, of the present invention, or fragments thereof may be useful in inhibiting proliferative cells or tissues through the induction of apoptosis. Said polypeptides may act either directly, or indirectly to induce apoptosis of proliferative cells and tissues, for example in the activation of a death-domain receptor, such as tumor necrosis factor (TNF) receptor-1, CD95 (Fas/APO-1), TNF-receptor-related apoptosis-mediated protein (TRAMP) and TNF-related apoptosis-inducing ligand (TRAIL) receptor-1 and -2 (See Schulze-Osthoff K, et. al., Eur J Biochem 254(3):439-59 (1998), which is hereby incorporated by reference). Moreover, in another preferred embodiment of the present invention, said polypeptides may induce apoptosis through other mechanisms, such as in the activation of other proteins which will activate apoptosis, or through stimulating the expression of said proteins, either alone or in combination with small molecule drugs or adjuviants, such as apoptonin, galectins, thioredoxins, antiinflammatory proteins (See for example, Mutat Res 400(1-2):447-55 (1998), Med Hypotheses.50(5):423-33 (1998), Chem Biol Interact. Apr 24;111-112:23-34 (1998), J Mol Med.76(6):402-12 (1998), Int J Tissue React;20(1):3-15 (1998), which are all hereby incorporated by reference).
Polypeptides, including protein fusions to, or fragments thereof, of the present invention are useful in inhibiting the metastasis of proliferative cells or tissues. Inhibition may occur as a direct result of administering polypeptides, or antibodies directed to said polypeptides as described elsewere herein, or indirectly, such as activating the expression of proteins known to inhibit metastasis, for example alpha 4 integrins, (See, e.g., Curr Top Microbiol Immunol 1998;231:125-41, which is hereby incorporated by reference). Such therapeutic affects of the present invention may be achieved either alone, or in combination with small molecule drugs or adjuvants.
In another embodiment, the invention provides a method of delivering compositions containing the polypeptides of the invention (e.g., compositions containing polypeptides or polypeptide antibodes associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs) to targeted cells expressing the polypeptide of the present invention. Polypeptides or polypeptide antibodes of the invention may be associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs via hydrophobic, hydrophilic, ionic and/or covalent interactions.
Polypeptides, protein fusions to, or fragments thereof, of the present invention are useful in enhancing the immunogenicity and/or antigenicity of proliferating cells or tissues, either directly, such as would occur if the polypeptides of the present invention xe2x80x98vaccinatedxe2x80x99 the immune response to respond to proliferative antigens and immunogens, or indirectly, such as in activating the expression of proteins known to enhance the immune response (e.g. chemokines), to said antigens and immunogens.
Cardiovascular Disorders
Polynucleotides or polypeptides, or agonists or antagonists of the invention may be used to treat, prevent, and/or diagnose cardiovascular diseases, disorders, and/or conditions, including peripheral artery disease, such as limb ischemia.
Cardiovascular diseases, disorders, and/or conditions include cardiovascular abnormalities, such as arterio-arterial fistula, arteriovenous fistula, cerebral arteriovenous malformations, congenital heart defects, pulmonary atresia, and Scimitar Syndrome. Congenital heart defects include aortic coarctation, cor triatriatum, coronary vessel anomalies, crisscross heart, dextrocardia, patent ductus arteriosus, Ebstein""s anomaly, Eisenmenger complex, hypoplastic left heart syndrome, levocardia, tetralogy of fallot, transposition of great vessels, double outlet right ventricle, tricuspid atresia, persistent truncus arteriosus, and heart septal defects, such as aortopulmonary septal defect, endocardial cushion defects, Lutembacher""s Syndrome, trilogy of Fallot, ventricular heart septal defects.
Cardiovascular diseases, disorders, and/or conditions also include heart disease, such as arrhythmias, carcinoid heart disease, high cardiac output, low cardiac output, cardiac tamponade, endocarditis (including bacterial), heart aneurysm, cardiac arrest, congestive heart failure, congestive cardiomyopathy, paroxysmal dyspnea, cardiac edema, heart hypertrophy, congestive cardiomyopathy, left ventricular hypertrophy, right ventricular hypertrophy, post-infarction heart rupture, ventricular septal rupture, heart valve diseases, myocardial diseases, myocardial ischemia, pericardial effusion, pericarditis (including constrictive and tuberculous), pneumopericardium, postpericardiotomy syndrome, pulmonary heart disease, rheumatic heart disease, ventricular dysfunction, hyperemia, cardiovascular pregnancy complications, Scimitar Syndrome, cardiovascular syphilis, and cardiovascular tuberculosis.
Arrhythmias include sinus arrhythmia, atrial fibrillation, atrial flutter, bradycardia, extrasystole, Adams-Stokes Syndrome, bundle-branch block, sinoatrial block, long QT syndrome, parasystole, Lown-Ganong-Levine Syndrome, Mahaim-type pre-excitation syndrome, Wolff-Parkinson-White syndrome, sick sinus syndrome, tachycardias, and ventricular fibrillation. Tachycardias include paroxysmal tachycardia, supraventricular tachycardia, accelerated idioventricular rhythm, atrioventricular nodal reentry tachycardia, ectopic atrial tachycardia, ectopic junctional tachycardia, sinoatrial nodal reentry tachycardia, sinus tachycardia, Torsades de Pointes, and ventricular tachycardia.
Heart valve disease include aortic valve insufficiency, aortic valve stenosis, hear murmurs, aortic valve prolapse, mitral valve prolapse, tricuspid valve prolapse, mitral valve insufficiency, mitral valve stenosis, pulmonary atresia, pulmonary valve insufficiency, pulmonary valve stenosis, tricuspid atresia, tricuspid valve insufficiency, and tricuspid valve stenosis.
Myocardial diseases include alcoholic cardiomyopathy, congestive cardiomyopathy, hypertrophic cardiomyopathy, aortic subvalvular stenosis, pulmonary subvalvular stenosis, restrictive cardiomyopathy, Chagas cardiomyopathy, endocardial fibroelastosis, endomyocardial fibrosis, Kearns Syndrome, myocardial reperfusion injury, and myocarditis.
Myocardial ischemias include coronary disease, such as angina pectoris, coronary aneurysm, coronary arteriosclerosis, coronary thrombosis, coronary vasospasm, myocardial infarction and myocardial stunning.
Cardiovascular diseases also include vascular diseases such as aneurysms, angiodysplasia, angiomatosis, bacillary angiomatosis, Hippel-Lindau Disease, Klippel-Trenaunay-Weber Syndrome, Sturge-Weber Syndrome, angioneurotic edema, aortic diseases, Takayasu""s Arteritis, aortitis, Leriche""s Syndrome, arterial occlusive diseases, arteritis, enarteritis, polyarteritis nodosa, cerebrovascular diseases, disorders, and/or conditions, diabetic angiopathies, diabetic retinopathy, embolisms, thrombosis, erythromelalgia, hemorrhoids, hepatic veno-occlusive disease, hypertension, hypotension, ischemia, peripheral vascular diseases, phlebitis, pulmonary veno-occlusive disease, Raynaud""s disease, CREST syndrome, retinal vein occlusion, Scimitar syndrome, superior vena cava syndrome, telangiectasia, atacia telangiectasia, hereditary hemorrhagic telangiectasia, varicocele, varicose veins, varicose ulcer, vasculitis, and venous insufficiency.
Aneurysms include dissecting aneurysms, false aneurysms, infected aneurysms, ruptured aneurysms, aortic aneurysms, cerebral aneurysms, coronary aneurysms, heart aneurysms, and iliac aneurysms.
Arterial occlusive diseases include arteriosclerosis, intermittent claudication, carotid stenosis, fibromuscular dysplasias, mesenteric vascular occlusion, Moyamoya disease, renal artery obstruction, retinal artery occlusion, and thromboangiitis obliterans.
Cerebrovascular diseases, disorders, and/or conditions include carotid artery diseases, cerebral amyloid angiopathy, cerebral aneurysm, cerebral anoxia, cerebral arteriosclerosis, cerebral arteriovenous malformation, cerebral artery diseases, cerebral embolism and thrombosis, carotid artery thrombosis, sinus thrombosis, Wallenberg""s syndrome, cerebral hemorrhage, epidural hematoma, subdural hematoma, subaraxhnoid hemorrhage, cerebral infarction, cerebral ischemia (including transient), subclavian steal syndrome, periventricular leukomalacia, vascular headache, cluster headache, migraine, and vertebrobasilar insufficiency.
Embolisms include air embolisms, amniotic fluid embolisms, cholesterol embolisms, blue toe syndrome, fat embolisms, pulmonary embolisms, and thromoboembolisms. Thrombosis include coronary thrombosis, hepatic vein thrombosis, retinal vein occlusion, carotid artery thrombosis, sinus thrombosis, Wallenberg""s syndrome, and thrombophlebitis.
Ischemia includes cerebral ischemia, ischemic colitis, compartment syndromes, anterior compartment syndrome, myocardial ischemia, reperfusion injuries, and peripheral limb ischemia. Vasculitis includes aortitis, arteritis, Behcet""s Syndrome, Churg-Strauss Syndrome, mucocutaneous lymph node syndrome, thromboangiitis obliterans, hypersensitivity vasculitis, Schoenlein-Henoch purpura, allergic cutaneous vasculitis, and Wegener""s granulomatosis.
Polynucleotides or polypeptides, or agonists or antagonists of the invention, are especially effective for the treatment of critical limb ischemia and coronary disease.
Polypeptides may be administered using any method known in the art, including, but not limited to, direct needle injection at the delivery site, intravenous injection, topical administration, catheter infusion, biolistic injectors, particle accelerators, gelfoam sponge depots, other commercially available depot materials, osmotic pumps, oral or suppositorial solid pharmaceutical formulations, decanting or topical applications during surgery, aerosol delivery. Such methods are known in the art. Polypeptides of the invention may be administered as part of a Therapeutic, described in more detail below. Methods of delivering polynucleotides of the invention are described in more detail herein.
Anti-Angiogenesis Activity
The naturally occurring balance between endogenous stimulators and inhibitors of angiogenesis is one in which inhibitory influences predominate. Rastinejad et al., Cell 56:345-355 (1989). In those rare instances in which neovascularization occurs under normal physiological conditions, such as wound healing, organ regeneration, embryonic development, and female reproductive processes, angiogenesis is stringently regulated and spatially and temporally delimited. Under conditions of pathological angiogenesis such as that characterizing solid tumor growth, these regulatory controls fail. Unregulated angiogenesis becomes pathologic and sustains progression of many neoplastic and non-neoplastic diseases. A number of serious diseases are dominated by abnormal neovascularization including solid tumor growth and metastases, arthritis, some types of eye diseases, disorders, and/or conditions, and psoriasis. See, e.g., reviews by Moses et al., Biotech. 9:630-634 (1991); Folkman et al., N. Engl. J Med., 333:1757-1763 (1995); Auerbach et al., J. Microvasc. Res. 29:401-411 (1985); Folkman, Advances in Cancer Research, eds. Klein and Weinhouse, Academic Press, New York, pp. 175-203 (1985); Patz, Am. J. Opthalmol. 94:715-743 (1982); and Folkman et al., Science 221:719-725 (1983). In a number of pathological conditions, the process of angiogenesis contributes to the disease state. For example, significant data have accumulated which suggest that the growth of solid tumors is dependent on angiogenesis. Folkman and Klagsbrun, Science 235:442-447 (1987).
The present invention provides for treatment of diseases, disorders, and/or conditions associated with neovascularization by administration of the polynucleotides and/or polypeptides of the invention, as well as agonists or antagonists of the present invention. Malignant and metastatic conditions which can be treated with the polynucleotides and polypeptides, or agonists or antagonists of the invention include, but are not limited to, malignancies, solid tumors, and cancers described herein and otherwise known in the art (for a review of such disorders, see Fishman et al., Medicine, 2d Ed., J. B. Lippincott Co., Philadelphia (1985)).Thus, the present invention provides a method of treating, preventing, and/or diagnosing an angiogenesis-related disease and/or disorder, comprising administering to an individual in need thereof a therapeutically effective amount of a polynucleotide, polypeptide, antagonist and/or agonist of the invention. For example, polynucleotides, polypeptides, antagonists and/or agonists may be utilized in a variety of additional methods in order to therapeutically treator prevent a cancer or tumor. Cancers which may be treated, prevented, and/or diagnosed with polynucleotides, polypeptides, antagonists and/or agonists include, but are not limited to solid tumors, including prostate, lung, breast, ovarian, stomach, pancreas, larynx, esophagus, testes, liver, parotid, biliary tract, colon, rectum, cervix, uterus, endometrium, kidney, bladder, thyroid cancer; primary tumors and metastases; melanomas; glioblastoma; Kaposi""s sarcoma; leiomyosarcoma; non-small cell lung cancer; colorectal cancer; advanced malignancies; and blood born tumors such as leukemias. For example, polynucleotides, polypeptides, antagonists and/or agonists may be delivered topically, in order to treat or prevent cancers such as skin cancer, head and neck tumors, breast tumors, and Kaposi""s sarcoma.
Within yet other aspects, polynucleotides, polypeptides, antagonists and/or agonists may be utilized to treat superficial forms of bladder cancer by, for example, intravesical administration. Polynucleotides, polypeptides, antagonists and/or agonists may be delivered directly into the tumor, or near the tumor site, via injection or a catheter. Of course, as the artisan of ordinary skill will appreciate, the appropriate mode of administration will vary according to the cancer to be treated. Other modes of delivery are discussed herein.
Polynucleotides, polypeptides, antagonists and/or agonists may be useful in treating, preventing, and/or diagnosing other diseases, disorders, and/or conditions, besides cancers, which involve angiogenesis. These diseases, disorders, and/or conditions include, but are not limited to: benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas; artheroscleric plaques; ocular angiogenic diseases, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, retrolental fibroplasia, rubeosis, retinoblastoma, uvietis and Pterygia (abnormal blood vessel growth) of the eye; rheumatoid arthritis; psoriasis; delayed wound healing; endometriosis; vasculogenesis; granulations; hypertrophic scars (keloids); nonunion fractures; scleroderma; trachoma; vascular adhesions; myocardial angiogenesis; coronary collaterals; cerebral collaterals; arteriovenous malformations; ischemic limb angiogenesis; Osler-Webber Syndrome; plaque neovascularization; telangiectasia; hemophiliac joints; angiofibroma; fibromuscular dysplasia; wound granulation; Crohn""s disease; and atherosclerosis.
For example, within one aspect of the present invention methods are provided for treating, preventing, and/or diagnosing hypertrophic scars and keloids, comprising the step of administering a polynucleotide, polypeptide, antagonist and/or agonist of the invention to a hypertrophic scar or keloid.
Within one embodiment of the present invention polynucleotides, polypeptides, antagonists and/or agonists are directly injected into a hypertrophic scar or keloid, in order to prevent the progression of these lesions. This therapy is of particular value in the prophylactic treatment of conditions which are known to result in the development of hypertrophic scars and keloids (e.g., burns), and is preferably initiated after the proliferative phase has had time to progress (approximately 14 days after the initial injury), but before hypertrophic scar or keloid development. As noted above, the present invention also provides methods for treating, preventing, and/or diagnosing neovascular diseases of the eye, including for example, corneal neovascularization, neovascular glaucoma, proliferative diabetic retinopathy, retrolental fibroplasia and macular degeneration.
Moreover, Ocular diseases, disorders, and/or conditions associated with neovascularization which can be treated, prevented, and/or diagnosed with the polynucleotides and polypeptides of the present invention (including agonists and/or antagonists) include, but are not limited to: neovascular glaucoma, diabetic retinopathy, retinoblastoma, retrolental fibroplasia, uveitis, retinopathy of prematurity macular degeneration, corneal graft neovascularization, as well as other eye inflammatory diseases, ocular tumors and diseases associated with choroidal or iris neovascularization. See, e.g., reviews by Waltman et al., Am. J. Ophthal. 85:704-710 (1978) and Gartner et al., Surv. Ophthal. 22:291-312 (1978).
Thus, within one aspect of the present invention methods are provided for treating or preventing neovascular diseases of the eye such as corneal neovascularization (including corneal graft neovascularization), comprising the step of administering to a patient a therapeutically effective amount of a compound (as described above) to the cornea, such that the formation of blood vessels is inhibited. Briefly, the cornea is a tissue which normally lacks blood vessels. In certain pathological conditions however, capillaries may extend into the cornea from the pericorneal vascular plexus of the limbus. When the cornea becomes vascularized, it also becomes clouded, resulting in a decline in the patient""s visual acuity. Visual loss may become complete if the cornea completely opacitates. A wide variety of diseases, disorders, and/or conditions can result in corneal neovascularization, including for example, corneal infections (e.g., trachoma, herpes simplex keratitis, leishmaniasis and onchocerciasis), immunological processes (e.g., graft rejection and Stevens-Johnson""s syndrome), alkali bums, trauma, inflammation (of any cause), toxic and nutritional deficiency states, and as a complication of wearing contact lenses.
Within particularly preferred embodiments of the invention, may be prepared for topical administration in saline (combined with any of the preservatives and antimicrobial agents commonly used in ocular preparations), and administered in eyedrop form. The solution or suspension may be prepared in its pure form and administered several times daily. Alternatively, anti-angiogenic compositions, prepared as described above, may also be administered directly to the cornea. Within preferred embodiments, the anti-angiogenic composition is prepared with a muco-adhesive polymer which binds to cornea. Within further embodiments, the anti-angiogenic factors or anti-angiogenic compositions may be utilized as an adjunct to conventional steroid therapy. Topical therapy may also be useful prophylactically in corneal lesions which are known to have a high probability of inducing an angiogenic response (such as chemical burns). In these instances the treatment, likely in combination with steroids, may be instituted immediately to help prevent subsequent complications.
Within other embodiments, the compounds described above may be injected directly into the corneal stroma by an ophthalmologist under microscopic guidance. The preferred site of injection may vary with the morphology of the individual lesion, but the goal of the administration would be to place the composition at the advancing front of the vasculature (i.e., interspersed between the blood vessels and the normal cornea). In most cases this would involve perilimbic corneal injection to xe2x80x9cprotectxe2x80x9d the cornea from the advancing blood vessels. This method may also be utilized shortly after a corneal insult in order to prophylactically prevent corneal neovascularization. In this situation the material could be injected in the perilimbic cornea interspersed between the corneal lesion and its undesired potential limbic blood supply. Such methods may also be utilized in a similar fashion to prevent capillary invasion of transplanted corneas. In a sustained-release form injections might only be required 2-3 times per year. A steroid could also be added to the injection solution to reduce inflammation resulting from the injection itself.
Within another aspect of the present invention, methods are provided for treating or preventing neovascular glaucoma, comprising the step of administering to a patient a therapeutically effective amount of a polynucleotide, polypeptide, antagonist and/or agonist to the eye, such that the formation of blood vessels is inhibited. In one embodiment, the compound may be administered topically to the eye in order to treat or prevent early forms of neovascular glaucoma. Within other embodiments, the compound may be implanted by injection into the region of the anterior chamber angle. Within other embodiments, the compound may also be placed in any location such that the compound is continuously released into the aqueous humor. Within another aspect of the present invention, methods are provided for treating or preventing proliferative diabetic retinopathy, comprising the step of administering to a patient a therapeutically effective amount of a polynucleotide, polypeptide, antagonist and/or agonist to the eyes, such that the formation of blood vessels is inhibited.
Within particularly preferred embodiments of the invention, proliferative diabetic retinopathy may be treated by injection into the aqueous humor or the vitreous, in order to increase the local concentration of the polynucleotide, polypeptide, antagonist and/or agonist in the retina. Preferably, this treatment should be initiated prior to the acquisition of severe disease requiring photocoagulation.
Within another aspect of the present invention, methods are provided for treating or preventing retrolental fibroplasia, comprising the step of administering to a patient a therapeutically effective amount of a polynucleotide, polypeptide, antagonist and/or agonist to the eye, such that the formation of blood vessels is inhibited. The compound may be administered topically, via intravitreous injection and/or via intraocular implants.
Additionally, diseases, disorders, and/or conditions which can be treated, prevented, and/or diagnosed with the polynucleotides, polypeptides, agonists and/or agonists include, but are not limited to, hemangioma, arthritis, psoriasis, angiofibroma, atherosclerotic plaques, delayed wound healing, granulations, hemophilic joints, hypertrophic scars, nonunion fractures, Osler-Weber syndrome, pyogenic granuloma, scleroderma, trachoma, and vascular adhesions.
Moreover, diseases, disorders, and/or conditions and/or states, which can be treated, prevented, and/or diagnosed with the polynucleotides, polypeptides, agonists and/or agonists include, but are not limited to, solid tumors, blood born tumors such as leukemias, tumor metastasis, Kaposi""s sarcoma, benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas, rheumatoid arthritis, psoriasis, ocular angiogenic diseases, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, retrolental fibroplasia, rubeosis, retinoblastoma, and uvietis, delayed wound healing, endometriosis, vascluogenesis, granulations, hypertrophic scars (keloids), nonunion fractures, scleroderma, trachoma, vascular adhesions, myocardial angiogenesis, coronary collaterals, cerebral collaterals, arteriovenous malformations, ischemic limb angiogenesis, Osler-Webber Syndrome, plaque neovascularization, telangiectasia, hemophiliac joints, angiofibroma fibromuscular dysplasia, wound granulation, Crohn""s disease, atherosclerosis, birth control agent by preventing vascularization required for embryo implantation controlling menstruation, diseases that have angiogenesis as a pathologic consequence such as cat scratch disease (Rochele minalia quintosa), ulcers (Helicobacter pylori), Bartonellosis and bacillary angiomatosis.
In one aspect of the birth control method, an amount of the compound sufficient to block embryo implantation is administered before or after intercourse and fertilization have occurred, thus providing an effective method of birth control, possibly a xe2x80x9cmorning afterxe2x80x9d method. Polynucleotides, polypeptides, agonists and/or agonists may also be used in controlling menstruation or administered as either a peritoneal lavage fluid or for peritoneal implantation in the treatment of endometriosis.
Polynucleotides, polypeptides, agonists and/or agonists of the present invention may be incorporated into surgical sutures in order to prevent stitch granulomas.
Polynucleotides, polypeptides, agonists and/or agonists may be utilized in a wide variety of surgical procedures. For example, within one aspect of the present invention a compositions (in the form of, for example, a spray or film) may be utilized to coat or spray an area prior to removal of a tumor, in order to isolate normal surrounding tissues from malignant tissue, and/or to prevent the spread of disease to surrounding tissues. Within other aspects of the present invention, compositions (e.g., in the form of a spray) may be delivered via endoscopic procedures in order to coat tumors, or inhibit angiogenesis in a desired locale. Within yet other aspects of the present invention, surgical meshes which have been coated with anti-angiogenic compositions of the present invention may be utilized in any procedure wherein a surgical mesh might be utilized. For example, within one embodiment of the invention a surgical mesh laden with an anti-angiogenic composition may be utilized during abdominal cancer resection surgery (e.g., subsequent to colon resection) in order to provide support to the structure, and to release an amount of the anti-angiogenic factor.
Within further aspects of the present invention, methods are provided for treating tumor excision sites, comprising administering a polynucleotide, polypeptide, agonist and/or agonist to the resection margins of a tumor subsequent to excision, such that the local recurrence of cancer and the formation of new blood vessels at the site is inhibited. Within one embodiment of the invention, the anti-angiogenic compound is administered directly to the tumor excision site (e.g., applied by swabbing, brushing or otherwise coating the resection margins of the tumor with the anti-angiogenic compound). Alternatively, the anti-angiogenic compounds may be incorporated into known surgical pastes prior to administration. Within particularly preferred embodiments of the invention, the anti-angiogenic compounds are applied after hepatic resections for malignancy, and after neurosurgical operations.
Within one aspect of the present invention, polynucleotides, polypeptides, agonists and/or agonists may be administered to the resection margin of a wide variety of tumors, including for example, breast, colon, brain and hepatic tumors. For example, within one embodiment of the invention, anti-angiogenic compounds may be administered to the site of a neurological tumor subsequent to excision, such that the formation of new blood vessels at the site are inhibited.
The polynucleotides, polypeptides, agonists and/or agonists of the present invention may also be administered along with other anti-angiogenic factors. Representative examples of other anti-angiogenic factors include: Anti-Invasive Factor, retinoic acid and derivatives thereof, paclitaxel, Suramin, Tissue Inhibitor of Metalloproteinase-1, Tissue Inhibitor of Metalloproteinase-2, Plasminogen Activator Inhibitor-1, Plasminogen Activator Inhibitor-2, and various forms of the lighter xe2x80x9cd groupxe2x80x9d transition metals.
Lighter xe2x80x9cd groupxe2x80x9d transition metals include, for example, vanadium, molybdenum, tungsten, titanium, niobium, and tantalum species. Such transition metal species may form transition metal complexes. Suitable complexes of the above-mentioned transition metal species include oxo transition metal complexes.
Representative examples of vanadium complexes include oxo vanadium complexes such as vanadate and vanadyl complexes. Suitable vanadate complexes include metavanadate and orthovanadate complexes such as, for example, ammonium metavanadate, sodium metavanadate, and sodium orthovanadate. Suitable vanadyl complexes include, for example, vanadyl acetylacetonate and vanadyl sulfate including vanadyl sulfate hydrates such as vanadyl sulfate mono- and trihydrates.
Representative examples of tungsten and molybdenum complexes also include oxo complexes. Suitable oxo tungsten complexes include tungstate and tungsten oxide complexes. Suitable tungstate complexes include ammonium tungstate, calcium tungstate, sodium tungstate dihydrate, and tungstic acid. Suitable tungsten oxides include tungsten (IV) oxide and tungsten (VI) oxide. Suitable oxo molybdenum complexes include molybdate, molybdenum oxide, and molybdenyl complexes. Suitable molybdate complexes include ammonium molybdate and its hydrates, sodium molybdate and its hydrates, and potassium molybdate and its hydrates. Suitable molybdenum oxides include molybdenum (VI) oxide, molybdenum (VI) oxide, and molybdic acid. Suitable molybdenyl complexes include, for example, molybdenyl acetylacetonate. Other suitable tungsten and molybdenum complexes include hydroxo derivatives derived from, for example, glycerol, tartaric acid, and sugars.
A wide variety of other anti-angiogenic factors may also be utilized within the context of the present invention. Representative examples include platelet factor 4; protamine sulphate; sulphated chitin derivatives (prepared from queen crab shells), (Murata et al., Cancer Res. 51:22-26, 1991); Sulphated Polysaccharide Peptidoglycan Complex (SP-PG) (the function of this compound may be enhanced by the presence of steroids such as estrogen, and tamoxifen citrate); Staurosporine; modulators of matrix metabolism, including for example, proline analogs, cishydroxyproline, d,L-3,4-dehydroproline, Thiaproline, alpha,alpha-dipyridyl, aminopropionitrile fumarate; 4-propyl-5-(4-pyridinyl)-2(3H)-oxazolone; Methotrexate; Mitoxantrone; Heparin; Interferons; 2 Macroglobulin-serum; ChIMP-3 (Pavloff et al., J. Bio. Chem. 267:17321-17326, 1992); Chymostatin (Tomkinson et al., Biochem J. 286:475-480, 1992); Cyclodextrin Tetradecasulfate; Eponemycin; Camptothecin; Fumagillin (Ingber et al., Nature 348:555-557, 1990); Gold Sodium Thiomalate (xe2x80x9cGSTxe2x80x9d; Matsubara and Ziff, J. Clin. Invest. 79:1440-1446, 1987); anticollagenase-serum; alpha2-antiplasmin (Holmes et al., J. Biol. Chem. 262(4):1659-1664, 1987); Bisantrene (National Cancer Institute); Lobenzarit disodium (N-(2)-carboxyphenyl-4-chloroanthronilic acid disodium or xe2x80x9cCCAxe2x80x9d; Takeuchi et al., Agents Actions 36:312-316, 1992); Thalidomide; Angostatic steroid; AGM-1470; carboxynaminolmidazole; and metalloproteinase inhibitors such as BB94.
Diseases at the Cellular Level
Diseases associated with increased cell survival or the inhibition of apoptosis that could be treated, prevented, and/or diagnosed by the polynucleotides or polypeptides and/or antagonists or agonists of the invention, include cancers (such as follicular lymphomas, carcinomas with p53 mutations, and hormone-dependent tumors, including, but not limited to colon cancer, cardiac tumors, pancreatic cancer, melanoma, retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicular cancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma, endothelioma, osteoblastoma, osteoclastoma, osteosarcoma, chondrosarcoma, adenoma, breast cancer, prostate cancer, Kaposi""s sarcoma and ovarian cancer); autoimmune diseases, disorders, and/or conditions (such as, multiple sclerosis, Sjogren""s syndrome, Hashimoto""s thyroiditis, biliary cirrhosis, Behcet""s disease, Crohn""s disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) and viral infections (such as herpes viruses, pox viruses and adenoviruses), inflammation, graft v. host disease, acute graft rejection, and chronic graft rejection. In preferred embodiments, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention are used to inhibit growth, progression, and/or metasis of cancers, in particular those listed above.
Additional diseases or conditions associated with increased cell survival that could be treated, prevented or diagnosed by the polynucleotides or polypeptides, or agonists or antagonists of the invention, include, but are not limited to, progression, and/or metastases of malignancies and related disorders such as leukemia (including acute leukemias (e.g., acute lymphocytic leukemia, acute myelocytic leukemia (including myeloblastic, promyelocytic, myelomonocytic, monocytic, and erythroleukemia)) and chronic leukemias (e.g., chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia)), polycythemia vera, lymphomas (e.g., Hodgkin""s disease and non-Hodgkin""s disease), multiple myeloma, Waldenstrom""s macroglobulinemia, heavy chain disease, and solid tumors including, but not limited to, sarcomas and carcinomas such as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing""s tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm""s tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, and retinoblastoma.
Diseases associated with increased apoptosis that could be treated, prevented, and/or diagnosed by the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, include AIDS; neurodegenerative diseases, disorders, and/or conditions (such as Alzheimer""s disease, Parkinson""s disease, Amyotrophic lateral sclerosis, Retinitis pigmentosa, Cerebellar degeneration and brain tumor or prior associated disease); autoimmune diseases, disorders, and/or conditions (such as, multiple sclerosis, Sjogren""s syndrome, Hashimoto""s thyroiditis, biliary cirrhosis, Behcet""s disease, Crohn""s disease, polymyositis, systemic lupus erythematosus and immune-related glomerulonephritis and rheumatoid arthritis) myelodysplastic syndromes (such as aplastic anemia), graft v. host disease, ischemic injury (such as that caused by myocardial infarction, stroke and reperfusion injury), liver injury (e.g., hepatitis related liver injury, ischemia/reperfusion injury, cholestosis (bile duct injury) and liver cancer); toxin-induced liver disease (such as that caused by alcohol), septic shock, cachexia and anorexia.
Wound Healing and Epithelial Cell Proliferation
In accordance with yet a further aspect of the present invention, there is provided a process for utilizing the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, for therapeutic purposes, for example, to stimulate epithelial cell proliferation and basal keratinocytes for the purpose of wound healing, and to stimulate hair follicle production and healing of dermal wounds. Polynucleotides or polypeptides, as well as agonists or antagonists of the invention, may be clinically useful in stimulating wound healing including surgical wounds, excisional wounds, deep wounds involving damage of the dermis and epidermis, eye tissue wounds, dental tissue wounds, oral cavity wounds, diabetic ulcers, dermal ulcers, cubitus ulcers, arterial ulcers, venous stasis ulcers, bums resulting from heat exposure or chemicals, and other abnormal wound healing conditions such as uremia, malnutrition, vitamin deficiencies and complications associated with systemic treatment with steroids, radiation therapy and antineoplastic drugs and antimetabolites. Polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to promote dermal reestablishment subsequent to dermal loss
The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to increase the adherence of skin grafts to a wound bed and to stimulate re-epithelialization from the wound bed. The following are a non-exhaustive list of grafts that polynucleotides or polypeptides, agonists or antagonists of the invention, could be used to increase adherence to a wound bed: autografts, artificial skin, allografts, autodermic graft, autoepdermic grafts, avacular grafts, Blair-Brown grafts, bone graft, brephoplastic grafts, cutis graft, delayed graft, dermic graft, epidermic graft, fascia graft, full thickness graft, heterologous graft, xenograft, homologous graft, hyperplastic graft, lamellar graft, mesh graft, mucosal graft, Ollier-Thiersch graft, omenpal graft, patch graft, pedicle graft, penetrating graft, split skin graft, thick split graft. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, can be used to promote skin strength and to improve the appearance of aged skin.
It is believed that the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, will also produce changes in hepatocyte proliferation, and epithelial cell proliferation in the lung, breast, pancreas, stomach, small intesting, and large intestine. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could promote proliferation of epithelial cells such as sebocytes, hair follicles, hepatocytes, type II pneumocytes, mucin-producing goblet cells, and other epithelial cells and their progenitors contained within the skin, lung, liver, and gastrointestinal tract. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may promote proliferation of endothelial cells, keratinocytes, and basal keratinocytes.
The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could also be used to reduce the side effects of gut toxicity that result from radiation, chemotherapy treatments or viral infections. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may have a cytoprotective effect on the small intestine mucosa. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, may also stimulate healing of mucositis (mouth ulcers) that result from chemotherapy and viral infections.
The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could further be used in full regeneration of skin in full and partial thickness skin defects, including burns, (i.e., repopulation of hair follicles, sweat glands, and sebaceous glands), treatment of other skin defects such as psoriasis. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to treat epidermolysis bullosa, a defect in adherence of the epidermis to the underlying dermis which results in frequent, open and painful blisters by accelerating reepithelialization of these lesions. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could also be used to treat gastric and doudenal ulcers and help heal by scar formation of the mucosal lining and regeneration of glandular mucosa and duodenal mucosal lining more rapidly. Inflammatory bowel diseases, such as Crohn""s disease and ulcerative colitis, are diseases which result in destruction of the mucosal surface of the small or large intestine, respectively. Thus, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to promote the resurfacing of the mucosal surface to aid more rapid healing and to prevent progression of inflammatory bowel disease. Treatment with the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, is expected to have a significant effect on the production of mucus throughout the gastrointestinal tract and could be used to protect the intestinal mucosa from injurious substances that are ingested or following surgery. The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to treat diseases associate with the under expression of the polynucleotides of the invention.
Moreover, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to prevent and heal damage to the lungs due to various pathological states. A growth factor such as the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, which could stimulate proliferation and differentiation and promote the repair of alveoli and brochiolar epithelium to prevent or treat acute or chronic lung damage. For example, emphysema, which results in the progressive loss of aveoli, and inhalation injuries, i.e., resulting from smoke inhalation and burns, that cause necrosis of the bronchiolar epithelium and alveoli could be effectively treated, prevented, and/or diagnosed using the polynucleotides or polypeptides, and/or agonists or antagonists of the invention. Also, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to stimulate the proliferation of and differentiation of type II pneumocytes, which may help treat or prevent disease such as hyaline membrane diseases, such as infant respiratory distress syndrome and bronchopulmonary displasia, in premature infants.
The polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could stimulate the proliferation and differentiation of hepatocytes and, thus, could be used to alleviate or treat liver diseases and pathologies such as fulminant liver failure caused by cirrhosis, liver damage caused by viral hepatitis and toxic substances (i.e., acetaminophen, carbon tetraholoride and other hepatotoxins known in the art).
In addition, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used treat or prevent the onset of diabetes mellitus. In patients with newly diagnosed Types I and II diabetes, where some islet cell function remains, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used to maintain the islet function so as to alleviate, delay or prevent permanent manifestation of the disease. Also, the polynucleotides or polypeptides, and/or agonists or antagonists of the invention, could be used as an auxiliary in islet cell transplantation to improve or promote islet cell function.
Neurological Diseases
Nervous system diseases, disorders, and/or conditions, which can be treated, prevented, and/or diagnosed with the compositions of the invention (e.g., polypeptides, polynucleotides, and/or agonists or antagonists), include, but are not limited to, nervous system injuries, and diseases, disorders, and/or conditions which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated, prevented, and/or diagnosed in a patient (including human and non-human mammalian patients) according to the invention, include but are not limited to, the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems: (1) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia; (2) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries; (3) malignant lesions, in which a portion of the nervous system is destroyed or injured by malignant tissue which is either a nervous system associated malignancy or a malignancy derived from non-nervous system tissue; (4) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster, or herpes simplex virus or with Lyme disease, tuberculosis, syphilis; (5) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson""s disease, Alzheimer""s disease, Huntington""s chorea, or amyotrophic lateral sclerosis (ALS); (6) lesions associated with nutritional diseases, disorders, and/or conditions, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration; (7) neurological lesions associated with systemic diseases including, but not limited to, diabetes (diabetic neuropathy, Bell""s palsy), systemic lupus erythematosus, carcinoma, or sarcoidosis; (8) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and (9) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including, but not limited to, multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multifocal leukoencephalopathy, and central pontine myelinolysis.
In a preferred embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to protect neural cells from the damaging effects of cerebral hypoxia. According to this embodiment, the compositions of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral hypoxia. In one aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral ischemia. In another aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with cerebral infarction. In another aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose or prevent neural cell injury associated with a stroke. In a further aspect of this embodiment, the polypeptides, polynucleotides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose neural cell injury associated with a heart attack.
The compositions of the invention which are useful for treating or preventing a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, compositions of the invention which elicit any of the following effects may be useful according to the invention: (1) increased survival time of neurons in culture; (2) increased sprouting of neurons in culture or in vivo; (3) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or (4) decreased symptoms of neuron dysfunction in vivo. Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may routinely be measured using a method set forth herein or otherwise known in the art, such as, for example, the method set forth in Arakawa et al. (J. Neurosci. 10:3507-3515 (1990)); increased sprouting of neurons may be detected by methods known in the art, such as, for example, the methods set forth in Pestronk et al. (Exp. Neurol. 70:65-82 (1980)) or Brown et al. (Ann. Rev. Neurosci. 4:17-42 (1981)); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., using techniques known in the art and depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.
In specific embodiments, motor neuron diseases, disorders, and/or conditions that may be treated, prevented, and/or diagnosed according to the invention include, but are not limited to, diseases, disorders, and/or conditions such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as diseases, disorders, and/or conditions that selectively affect neurons such as amyotrophic lateral sclerosis, and including, but not limited to, progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).
Further, polypeptides or polynucleotides of the invention may play a role in neuronal survival; synapse formation; conductance; neural differentiation, etc. Thus, compositions of the invention (including polynucleotides, polypeptides, and agonists or antagonists) may be used to diagnose and/or treat or prevent diseases or disorders associated with these roles, including, but not limited to, learning and/or cognition disorders. The compositions of the invention may also be useful in the treatment or prevention of neurodegenerative disease states and/or behavioural disorders. Such neurodegenerative disease states and/or behavioral disorders include, but are not limited to, Alzheimers Disease, Parkinsons Disease, Huntingtons Disease, Tourette Syndrome, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, panic disorder, learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and perception. In addition, compositions of the invention may also play a role in the treatment, prevention and/or detection of developmental disorders associated with the developing embryo, or sexually-linked disorders.
Additionally, polypeptides, polynucleotides and/or agonists or antagonists of the invention, may be useful in protecting neural cells from diseases, damage, disorders, or injury, associated with cerebrovascular disorders including, but not limited to, carotid artery diseases (e.g., carotid artery thrombosis, carotid stenosis, or Moyamoya Disease), cerebral amyloid angiopathy, cerebral aneurysm, cerebral anoxia, cerebral arteriosclerosis, cerebral arteriovenous malformations, cerebral artery diseases, cerebral embolism and thrombosis (e.g., carotid artery thrombosis, sinus thrombosis, or Wallenberg""s Syndrome), cerebral hemorrhage (e.g., epidural or subdural hematoma, or subarachnoid hemorrhage), cerebral infarction, cerebral ischemia (e.g., transient cerebral ischemia, Subclavian Steal Syndrome, or vertebrobasilar insufficiency), vascular dementia (e.g., multi-infarct), leukomalacia, periventricular, and vascular headache (e.g., cluster headache or migraines).
In accordance with yet a further aspect of the present invention, there is provided a process for utilizing polynucleotides or polypeptides, as well as agonists or antagonists of the present invention, for therapeutic purposes, for example, to stimulate neurological cell proliferation and/or differentiation. Therefore, polynucleotides, polypeptides, agonists and/or antagonists of the invention may be used to treat and/or detect neurologic diseases. Moreover, polynucleotides or polypeptides, or agonists or antagonists of the invention, can be used as a marker or detector of a particular nervous system disease or disorder.
Examples of neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include brain diseases, such as metabolic brain diseases which includes phenylketonuria such as maternal phenylketonuria, pyruvate carboxylase deficiency, pyruvate dehydrogenase complex deficiency, Wernicke""s Encephalopathy, brain edema, brain neoplasms such as cerebellar neoplasms which include infratentorial neoplasms, cerebral ventricle neoplasms such as choroid plexus neoplasms, hypothalamic neoplasms, supratentorial neoplasms, canavan disease, cerebellar diseases such as cerebellar ataxia which include spinocerebellar degeneration such as ataxia telangiectasia, cerebellar dyssynergia, Friederich""s Ataxia, Machado-Joseph Disease, olivopontocerebellar atrophy, cerebellar neoplasms such as infratentorial neoplasms, diffuse cerebral sclerosis such as encephalitis periaxialis, globoid cell leukodystrophy, metachromatic leukodystrophy and subacute sclerosing panencephalitis.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include cerebrovascular disorders (such as carotid artery diseases which include carotid artery thrombosis, carotid stenosis and Moyamoya Disease), cerebral amyloid angiopathy, cerebral aneurysm, cerebral anoxia, cerebral arteriosclerosis, cerebral arteriovenous malformations, cerebral artery diseases, cerebral embolism and thrombosis such as carotid artery thrombosis, sinus thrombosis and Wallenberg""s Syndrome, cerebral hemorrhage such as epidural hematoma, subdural hematoma and subarachnoid hemorrhage, cerebral infarction, cerebral ischemia such as transient cerebral ischemia, Subclavian Steal Syndrome and vertebrobasilar insufficiency, vascular dementia such as multi-infarct dementia, periventricular leukomalacia, vascular headache such as cluster headache and migraine.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include dementia such as AIDS Dementia Complex, presenile dementia such as Alzheimer""s Disease and Creutzfeldt-Jakob Syndrome, senile dementia such as Alzheimer""s Disease and progressive supranuclear palsy, vascular dementia such as multi-infarct dementia, encephalitis which include encephalitis periaxialis, viral encephalitis such as epidemic encephalitis, Japanese Encephalitis, St. Louis Encephalitis, tick-borne encephalitis and West Nile Fever, acute disseminated encephalomyelitis, meningoencephalitis such as uveomeningoencephalitic syndrome, Postencephalitic Parkinson Disease and subacute sclerosing panencephalitis, encephalomalacia such as periventricular leukomalacia, epilepsy such as generalized epilepsy which includes infantile spasms, absence epilepsy, myoclonic epilepsy which includes MERRF Syndrome, tonic-clonic epilepsy, partial epilepsy such as complex partial epilepsy, frontal lobe epilepsy and temporal lobe epilepsy, post-traumatic epilepsy, status epilepticus such as Epilepsia Partialis Continua, and Hallervorden-Spatz Syndrome.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include hydrocephalus such as Dandy-Walker Syndrome and normal pressure hydrocephalus, hypothalamic diseases such as hypothalamic neoplasms, cerebral malaria, narcolepsy which includes cataplexy, bulbar poliomyelitis, cerebri pseudotumor, Rett Syndrome, Reye""s Syndrome, thalamic diseases, cerebral toxoplasmosis, intracranial tuberculoma and Zellweger Syndrome, central nervous system infections such as AIDS Dementia Complex, Brain Abscess, subdural empyema, encephalomyelitis such as Equine Encephalomyelitis, Venezuelan Equine Encephalomyelitis, Necrotizing Hemorrhagic Encephalomyelitis, Visna, and cerebral malaria.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include meningitis such as arachnoiditis, aseptic meningtitis such as viral meningtitis which includes lymphocytic choriomeningitis, Bacterial meningtitis which includes Haemophilus Meningtitis, Listeria Meningtitis, Meningococcal Meningtitis such as Waterhouse-Friderichsen Syndrome, Pneumococcal Meningtitis and meningeal tuberculosis, fungal meningitis such as Cryptococcal Meningtitis, subdural effusion, meningoencephalitis such as uvemeningoencephalitic syndrome, myelitis such as transverse myelitis, neurosyphilis such as tabes dorsalis, poliomyelitis which includes bulbar poliomyelitis and postpoliomyelitis syndrome, prion diseases (such as Creutzfeldt-Jakob Syndrome, Bovine Spongiform Encephalopathy, Gerstmann-Straussler Syndrome, Kuru, Scrapie), and cerebral toxoplasmosis.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include central nervous system neoplasms such as brain neoplasms that include cerebellar neoplasms such as infratentorial neoplasms, cerebral ventricle neoplasms such as choroid plexus neoplasms, hypothalamic neoplasms and supratentorial neoplasms, meningeal neoplasms, spinal cord neoplasms which include epidural neoplasms, demyelinating diseases such as Canavan Diseases, diffuse cerebral sceloris which includes adrenoleukodystrophy, encephalitis periaxialis, globoid cell leukodystrophy, diffuse cerebral sclerosis such as metachromatic leukodystrophy, allergic encephalomyelitis, necrotizing hemorrhagic encephalomyelitis, progressive multifocal leukoencephalopathy, multiple sclerosis, central pontine myelinolysis, transverse myelitis, neuromyelitis optica, Scrapie, Swayback, Chronic Fatigue Syndrome, Visna, High Pressure Nervous Syndrome, Meningism, spinal cord diseases such as amyotonia congenita, amyotrophic lateral sclerosis, spinal muscular atrophy such as Werdnig-Hoffmnann Disease, spinal cord compression, spinal cord neoplasms such as epidural neoplasms, syringomyelia, Tabes Dorsalis, Stiff-Man Syndrome, mental retardation such as Angelman Syndrome, Cri-du-Chat Syndrome, De Lange""s Syndrome, Down Syndrome, Gangliosidoses such as gangliosidoses G(M1), Sandhoff Disease, Tay-Sachs Disease, Hartnup Disease, homocystinuria, Laurence-Moon-Biedl Syndrome, Lesch-Nyhan Syndrome, Maple Syrup Urine Disease, mucolipidosis such as fucosidosis, neuronal ceroid-lipofuscinosis, oculocerebrorenal syndrome, phenylketonuria such as maternal phenylketonuria, Prader-Willi Syndrome, Rett Syndrome, Rubinstein-Taybi Syndrome, Tuberous Sclerosis, WAGR Syndrome, nervous system abnormalities such as holoprosencephaly, neural tube defects such as anencephaly which includes hydrangencephaly, Arnold-Chairi Deformity, encephalocele, meningocele, meningomyelocele, spinal dysraphism such as spina bifida cyistica and spina bifida occulta.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include hereditary motor and sensory neuropathies which include Charcot-Marie Disease, Hereditary optic atrophy, Refsum""s Disease, hereditary spastic paraplegia, Werdnig-Hoffmann Disease, Hereditary Sensory and Autonomic Neuropathies such as Congenital Analgesia and Familial Dysautonomia, Neurologic manifestations (such as agnosia that include Gerstmann""s Syndrome, Amnesia such as retrograde amnesia, apraxia, neurogenic bladder, cataplexy, communicative disorders such as hearing disorders that includes deafness, partial hearing loss, loudness recruitment and tinnitus, language disorders such as aphasia which include agraphia, anomia, broca aphasia, and Wernicke Aphasia, Dyslexia such as Acquired Dyslexia, language development disorders, speech disorders such as aphasia which includes anomia, broca aphasia and Wernicke Aphasia, articulation disorders, communicative disorders such as speech disorders which include dysarthria, echolalia, mutism and stuttering, voice disorders such as aphonia and hoarseness, decerebrate state, delirium, fasciculation, hallucinations, meningism, movement disorders such as angelman syndrome, ataxia, athetosis, chorea, dystonia, hypokinesia, muscle hypotonia, myoclonus, tic, torticollis and tremor, muscle hypertonia such as muscle rigidity such as stiff-man syndrome, muscle spasticity, paralysis such as facial paralysis which includes Herpes Zoster Oticus, Gastroparesis, Hemiplegia, ophthalmoplegia such as diplopia, Duane""s Syndrome, Homer""s Syndrome, Chronic progressive external ophthalmoplegia such as Kearns Syndrome, Bulbar Paralysis, Tropical Spastic Paraparesis, Paraplegia such as Brown-Sequard Syndrome, quadriplegia, respiratory paralysis and vocal cord paralysis, paresis, phantom limb, taste disorders such as ageusia and dysgeusia, vision disorders such as amblyopia, blindness, color vision defects, diplopia, hemianopsia, scotoma and subnormal vision, sleep disorders such as hypersomnia which includes Kleine-Levin Syndrome, insomnia, and somnambulism, spasm such as trismus, unconsciousness such as coma, persistent vegetative state and syncope and vertigo, neuromuscular diseases such as amyotonia congenita, amyotrophic lateral sclerosis, Lambert-Eaton Myasthenic Syndrome, motor neuron disease, muscular atrophy such as spinal muscular atrophy, Charcot-Marie Disease and Werdnig-Hoffmann Disease, Postpoliomyelitis Syndrome, Muscular Dystrophy, Myasthenia Gravis, Myotonia Atrophica, Myotonia Confenita, Nemaline Myopathy, Familial Periodic Paralysis, Multiplex Paramyloclonus, Tropical Spastic Paraparesis and Stiff-Man Syndrome, peripheral nervous system diseases such as acrodynia, amyloid neuropathies, autonomic nervous system diseases such as Adie""s Syndrome, Barre-Lieou Syndrome, Familial Dysautonomia, Horner""s Syndrome, Reflex Sympathetic Dystrophy and Shy-Drager Syndrome, Cranial Nerve Diseases such as Acoustic Nerve Diseases such as Acoustic Neuroma which includes Neurofibromatosis 2, Facial Nerve Diseases such as Facial Neuralgia, Melkersson-Rosenthal Syndrome, ocular motility disorders which includes amblyopia, nystagmus, oculomotor nerve paralysis, ophthalmoplegia such as Duane""s Syndrome, Homer""s Syndrome, Chronic Progressive External Ophthalmoplegia which includes Kearns Syndrome, Strabismus such as Esotropia and Exotropia, Oculomotor Nerve Paralysis, Optic Nerve Diseases such as Optic Atrophy which includes Hereditary Optic Atrophy, Optic Disk Drusen, Optic Neuritis such as Neuromyelitis Optica, Papilledema, Trigeminal Neuralgia, Vocal Cord Paralysis, Demyelinating Diseases such as Neuromyelitis Optica and Swayback, and Diabetic neuropathies such as diabetic foot.
Additional neurologic diseases which can be treated or detected with polynucleotides, polypeptides, agonists, and/or antagonists of the present invention include nerve compression syndromes such as carpal tunnel syndrome, tarsal tunnel syndrome, thoracic outlet syndrome such as cervical rib syndrome, ulnar nerve compression syndrome, neuralgia such as causalgia, cervico-brachial neuralgia, facial neuralgia and trigeminal neuralgia, neuritis such as experimental allergic neuritis, optic neuritis, polyneuritis, polyradiculoneuritis and radiculities such as polyradiculitis, hereditary motor and sensory neuropathies such as Charcot-Marie Disease, Hereditary Optic Atrophy, Refsum""s Disease, Hereditary Spastic Paraplegia and Werdnig-Hoffmnann Disease, Hereditary Sensory and Autonomic Neuropathies which include Congenital Analgesia and Familial Dysautonomia, POEMS Syndrome, Sciatica, Gustatory Sweating and Tetany).
Infectious Disease
A polypeptide or polynucleotide and/or agonist or antagonist of the present invention can be used to treat, prevent, and/or diagnose infectious agents. For example, by increasing the immune response, particularly increasing the proliferation and differentiation of B and/or T cells, infectious diseases may be treated, prevented, and/or diagnosed. The immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, polypeptide or polynucleotide and/or agonist or antagonist of the present invention may also directly inhibit the infectious agent, without necessarily eliciting an immune response.
Viruses are one example of an infectious agent that can cause disease or symptoms that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention. Examples of viruses, include, but are not limited to Examples of viruses, include, but are not limited to the following DNA and RNA viruses and viral families: Arbovirus, Adenoviridae, Arenaviridae, Arterivirus, Birnaviridae, Bunyaviridae, Caliciviridae, Circoviridae, Coronaviridae, Dengue, EBV, HIV, Flaviviridae, Hepadnaviridae (Hepatitis), Herpesviridae (such as, Cytomegalovirus, Herpes Simplex, Herpes Zoster), Mononegavirus (e.g., Paramyxoviridae, Morbillivirus, Rhabdoviridae), Orthomyxoviridae (e.g., Influenza A, Influenza B, and parainfluenza), Papiloma virus, Papovaviridae, Parvoviridae, Picornaviridae, Poxyiridae (such as Smallpox or Vaccinia), Reoviridae (e.g., Rotavirus), Retroviridae (HTLV-I, HTLV-II, Lentivirus), and Togaviridae (e.g., Rubivirus). Viruses falling within these families can cause a variety of diseases or symptoms, including, but not limited to: arthritis, bronchiollitis, respiratory syncytial virus, encephalitis, eye infections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome, hepatitis (A, B, C, E, Chronic Active, Delta), Japanese B encephalitis, Junin, Chikungunya, Rift Valley fever, yellow fever, meningitis, opportunistic infections (e.g., AIDS), pneumonia, Burkitt""s Lymphoma, chickenpox, hemorrhagic fever, Measles, Mumps, Parainfluenza, Rabies, the common cold, Polio, leukemia, Rubella, sexually transmitted diseases, skin diseases (e.g., Kaposi""s, warts), and viremia. polynucleotides or polypeptides, or agonists or antagonists of the invention, can be used to treat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose: meningitis, Dengue, EBV, and/or hepatitis (e.g., hepatitis B). In an additional specific embodiment polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat patients nonresponsive to one or more other commercially available hepatitis vaccines. In a further specific embodiment polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose AIDS.
Similarly, bacterial or fungal agents that can cause disease or symptoms and that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention include, but not limited to, include, but not limited to, the following Gram-Negative and Gram-positive bacteria and bacterial families and fungi: Actinomycetales (e.g., Corynebacterium, Mycobacterium, Norcardia), Cryptococcus neoformans, Aspergillosis, Bacillaceae (e.g., Anthrax, Clostridium), Bacteroidaceae, Blastomycosis, Bordetella, Borrelia (e.g., Borrelia burgdorferi), Brucellosis, Candidiasis, Campylobacter, Coccidioidomycosis, Cryptococcosis, Dermatocycoses, E. coli (e.g., Enterotoxigenic E. coli and Enterohemorrhagic E. coli), Enterobacteriaceae (Klebsiella, Salmonella (e.g., Salmonella typhi, and Salmonella paratyphi), Serratia, Yersinia), Erysipelothrix, Helicobacter, Legionellosis, Leptospirosis, Listeria, Mycoplasmatales, Mycobacterium leprae, Vibrio cholerae, Neisseriaceae (e.g., Acinetobacter, Gonorrhea, Menigococcal), Meisseria meningitidis, Pasteurellacea Infections (e.g., Actinobacillus, Heamophilus (e.g., Heamophilus influenza type B), Pasteurella), Pseudomonas, Rickettsiaceae, Chlamydiaceae, Syphilis, Shigella spp., Staphylococcal, Meningiococcal, Pneumococcal and Streptococcal (e.g., Streptococcus pneumoniae and Group B Streptococcus). These bacterial or fungal families can cause the following diseases or symptoms, including, but not limited to: bacteremia, endocarditis, eye infections (conjunctivitis, tuberculosis, uveitis), gingivitis, opportunistic infections (e.g., AIDS related infections), paronychia, prosthesis-related infections, Reiter""s Disease, respiratory tract infections, such as Whooping Cough or Empyema, sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery, Paratyphoid Fever, food poisoning, Typhoid, pneumonia, Gonorrhea, meningitis (e.g., mengitis types A and B), Chlamydia, Syphilis, Diphtheria, Leprosy, Paratuberculosis, Tuberculosis, Lupus, Botulism, gangrene, tetanus, impetigo, Rheumatic Fever, Scarlet Fever, sexually transmitted diseases, skin diseases (e.g., cellulitis, dermatocycoses), toxemia, urinary tract infections, wound infections. Polynucleotides or polypeptides, agonists or antagonists of the invention, can be used to treat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, agonists or antagonists of the invention are used to treat, prevent, and/or diagnose: tetanus, Diptheria, botulism, and/or meningitis type B.
Moreover, parasitic agents causing disease or symptoms that can be treated, prevented, and/or diagnosed by a polynucleotide or polypeptide and/or agonist or antagonist of the present invention include, but not limited to, the following families or class: Amebiasis, Babesiosis, Coccidiosis, Cryptosporidiosis, Dientamoebiasis, Dourine, Ectoparasitic, Giardiasis, Helminthiasis, Leishmaniasis, Theileriasis, Toxoplasmosis, Trypanosomiasis, and Trichomonas and Sporozoans (e.g., Plasmodium virax, Plasmodium falciparium, Plasmodium malariae and Plasmodium ovale). These parasites can cause a variety of diseases or symptoms, including, but not limited to: Scabies, Trombiculiasis, eye infections, intestinal disease (e.g., dysentery, giardiasis), liver disease, lung disease, opportunistic infections (e.g., AIDS related), malaria, pregnancy complications, and toxoplasmosis. polynucleotides or polypeptides, or agonists or antagonists of the invention, can be used to treat, prevent, and/or diagnose any of these symptoms or diseases. In specific embodiments, polynucleotides, polypeptides, or agonists or antagonists of the invention are used to treat, prevent, and/or diagnose malaria.
Preferably, treatment or prevention using a polypeptide or polynucleotide and/or agonist or antagonist of the present invention could either be by administering an effective amount of a polypeptide to the patient, or by removing cells from the patient, supplying the cells with a polynucleotide of the present invention, and returning the engineered cells to the patient (ex vivo therapy). Moreover, the polypeptide or polynucleotide of the present invention can be used as an antigen in a vaccine to raise an immune response against infectious disease.
Regeneration
A polynucleotide or polypeptide and/or agonist or antagonist of the present invention can be used to differentiate, proliferate, and attract cells, leading to the regeneration of tissues. (See, Science 276:59-87 (1997).) The regeneration of tissues could be used to repair, replace, or protect tissue damaged by congenital defects, trauma (wounds, bums, incisions, or ulcers), age, disease (e.g. osteoporosis, osteocarthritis, periodontal disease, liver failure), surgery, including cosmetic plastic surgery, fibrosis, reperfusion injury, or systemic cytokine damage.
Tissues that could be regenerated using the present invention include organs (e.g., pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac), vasculature (including vascular and lymphatics), nervous, hematopoietic, and skeletal (bone, cartilage, tendon, and ligament) tissue. Preferably, regeneration occurs without or decreased scarring. Regeneration also may include angiogenesis.
Moreover, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase regeneration of tissues difficult to heal. For example, increased tendon/ligament regeneration would quicken recovery time after damage. A polynucleotide or polypeptide and/or agonist or antagonist of the present invention could also be used prophylactically in an effort to avoid damage. Specific diseases that could be treated, prevented, and/or diagnosed include of tendinitis, carpal tunnel syndrome, and other tendon or ligament defects. A further example of tissue regeneration of non-healing wounds includes pressure ulcers, ulcers associated with vascular insufficiency, surgical, and traumatic wounds.
Similarly, nerve and brain tissue could also be regenerated by using a polynucleotide or polypeptide and/or agonist or antagonist of the present invention to proliferate and differentiate nerve cells. Diseases that could be treated, prevented, and/or diagnosed using this method include central and peripheral nervous system diseases, neuropathies, or mechanical and traumatic diseases, disorders, and/or conditions (e.g., spinal cord disorders, head trauma, cerebrovascular disease, and stoke). Specifically, diseases associated with peripheral nerve injuries, peripheral neuropathy (e.g., resulting from chemotherapy or other medical therapies), localized neuropathies, and central nervous system diseases (e.g., Alzheimer""s disease, Parkinson""s disease, Huntington""s disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome), could all be treated, prevented, and/or diagnosed using the polynucleotide or polypeptide and/or agonist or antagonist of the present invention.
Chemotaxis
A polynucleotide or polypeptide and/or agonist or antagonist of the present invention may have chemotaxis activity. A chemotaxic molecule attracts or mobilizes cells (e.g., monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells) to a particular site in the body, such as inflammation, infection, or site of hyperproliferation. The mobilized cells can then fight off and/or heal the particular trauma or abnormality.
A polynucleotide or polypeptide and/or agonist or antagonist of the present invention may increase chemotaxic activity of particular cells. These chemotactic molecules can then be used to treat, prevent, and/or diagnose inflammation, infection, hyperproliferative diseases, disorders, and/or conditions, or any immune system disorder by increasing the number of cells targeted to a particular location in the body. For example, chemotaxic molecules can be used to treat, prevent, and/or diagnose wounds and other trauma to tissues by attracting immune cells to the injured location. Chemotactic molecules of the present invention can also attract fibroblasts, which can be used to treat, prevent, and/or diagnose wounds.
It is also contemplated that a polynucleotide or polypeptide and/or agonist or antagonist of the present invention may inhibit chemotactic activity. These molecules could also be used to treat, prevent, and/or diagnose diseases, disorders, and/or conditions. Thus, a polynucleotide or polypeptide and/or agonist or antagonist of the present invention could be used as an inhibitor of chemotaxis.
Binding Activity
A polypeptide of the present invention may be used to screen for molecules that bind to the polypeptide or for molecules to which the polypeptide binds. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the molecule bound. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.
Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a fragment of the ligand, or a natural substrate, a ligand, a structural or functional mimetic. (See, Coligan et al., Current Protocols in Immunology 1(2):Chapter 5 (1991).) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or at least, a fragment of the receptor capable of being bound by the polypeptide (e.g., active site). In either case, the molecule can be rationally designed using known techniques.
Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide (or cell membrane containing the expressed polypeptide) are then preferably contacted with a test compound potentially containing the molecule to observe binding, stimulation, or inhibition of activity of either the polypeptide or the molecule.
The assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a label, or in an assay involving competition with a labeled competitor. Further, the assay may test whether the candidate compound results in a signal generated by binding to the polypeptide.
Alternatively, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
Preferably, an ELISA assay can measure polypeptide level or activity in a sample (e.g., biological sample) using a monoclonal or polyclonal antibody. The antibody can measure polypeptide level or activity by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
Additionally, the receptor to which a polypeptide of the invention binds can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting (Coligan, et al., Current Protocols in Immun., 1(2), Chapter 5, (1991)). For example, expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the polypeptides, for example, NIH3T3 cells which are known to contain multiple receptors for the FGF family proteins, and SC-3 cells, and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the polypeptides. Transfected cells which are grown on glass slides are exposed to the polypeptide of the present invention, after they have been labelled. The polypeptides can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase.
Following fixation and incubation, the slides are subjected to auto-radiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an iterative sub-pooling and re-screening process, eventually yielding a single clones that encodes the putative receptor.
As an alternative approach for receptor identification, the labeled polypeptides can be photoaffinity linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE analysis and exposed to X-ray film. The labeled complex containing the receptors of the polypeptides can be excised, resolved into peptide fragments, and subjected to protein microsequencing. The amino acid sequence obtained from microsequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the genes encoding the putative receptors.
Moreover, the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as xe2x80x9cDNA shufflingxe2x80x9d) may be employed to modulate the activities of polypeptides of the invention thereby effectively generating agonists and antagonists of polypeptides of the invention. See generally, U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252, and 5,837,458, and Patten, P. A., et al., Curr. Opinion Biotechnol. 8:724-33 (1997); Harayama, S. Trends Biotechnol. 16(2):76-82 (1998); Hansson, L. O., et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo, M. M. and Blasco, R. Biotechniques 24(2):308-13 (1998) (each of these patents and publications are hereby incorporated by reference). In one embodiment, alteration of polynucleotides and corresponding polypeptides of the invention may be achieved by DNA shuffling. DNA shuffling involves the assembly of two or more DNA segments into a desired polynucleotide sequence of the invention molecule by homologous, or site-specific, recombination. In another embodiment, polynucleotides and corresponding polypeptides of the invention may be alterred by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods prior to recombination. In another embodiment, one or more components, motifs, sections, parts, domains, fragments, etc., of the polypeptides of the invention may be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous molecules. In preferred embodiments, the heterologous molecules are family members. In further preferred embodiments, the heterologous molecule is a growth factor such as, for example, platelet-derived growth factor (PDGF), insulin-like growth factor (IGF-I), transforming growth factor (TGF)-alpha, epidermnal growth factor (EGF), fibroblast growth factor (FGF), TGF-beta, bone morphogenetic protein (BMP)-2, BMP-4, BMP-5, BMP-6, BMP-7, activins A and B, decapentaplegic(dpp), 60A, OP-2, dorsalin, growth differentiation factors (GDFs), nodal, MIS, inhibin-alpha, TGF-beta1, TGF-beta2, TGF-beta3, TGF-beta5, and glial-derived neurotrophic factor (GDNF).
Other preferred fragments are biologically active fragments of the polypeptides of the invention. Biologically active fragments are those exhibiting activity similar, but not necessarily identical, to an activity of the polypeptide. The biological activity of the fragments may include an improved desired activity, or a decreased undesirable activity.
Additionally, this invention provides a method of screening compounds to identify those which modulate the action of the polypeptide of the present invention. An example of such an assay comprises combining a mammalian fibroblast cell, a the polypeptide of the present invention, the compound to be screened and 3[H] thymidine under cell culture conditions where the fibroblast cell would normally proliferate. A control assay may be performed in the absence of the compound to be screened and compared to the amount of fibroblast proliferation in the presence of the compound to determine if the compound stimulates proliferation by determining the uptake of 3[H] thymidine in each case. The amount of fibroblast cell proliferation is measured by liquid scintillation chromatography which measures the incorporation of 3[H] thymidine. Both agonist and antagonist compounds may be identified by this procedure.
In another method, a mammalian cell or membrane preparation expressing a receptor for a polypeptide of the present invention is incubated with a labeled polypeptide of the present invention in the presence of the compound. The ability of the compound to enhance or block this interaction could then be measured. Alternatively, the response of a known second messenger system following interaction of a compound to be screened and the receptor is measured and the ability of the compound to bind to the receptor and elicit a second messenger response is measured to determine if the compound is a potential agonist or antagonist. Such second messenger systems include but are not limited to, cAMP guanylate cyclase, ion channels or phosphoinositide hydrolysis.
All of these above assays can be used as diagnostic or prognostic markers. The molecules discovered using these assays can be used to treat, prevent, and/or diagnose disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptides of the invention from suitably manipulated cells or tissues. Therefore, the invention includes a method of identifying compounds which bind to the polypeptides of the invention comprising the steps of: (a) incubating a candidate binding compound with the polypeptide; and (b) determining if binding has occurred. Moreover, the invention includes a method of identifying agonists/antagonists comprising the steps of: (a) incubating a candidate compound with the polypeptide, (b) assaying a biological activity, and (b) determining if a biological activity of the polypeptide has been altered.
Also, one could identify molecules bind a polypeptide of the invention experimentally by using the beta-pleated sheet regions contained in the polypeptide sequence of the protein. Accordingly, specific embodiments of the invention are directed to polynucleotides encoding polypeptides which comprise, or alternatively consist of, the amino acid sequence of each beta pleated sheet regions in a disclosed polypeptide sequence. Additional embodiments of the invention are directed to polynucleotides encoding polypeptides which comprise, or alternatively consist of, any combination or all of contained in the polypeptide sequences of the invention. Additional preferred embodiments of the invention are directed to polypeptides which comprise, or alternatively consist of, the amino acid sequence of each of the beta pleated sheet regions in one of the polypeptide sequences of the invention. Additional embodiments of the invention are directed to polypeptides which comprise, or alternatively consist of, any combination or all of the beta pleated sheet regions in one of the polypeptide sequences of the invention.
Targeted Delivery
In another embodiment, the invention provides a method of delivering compositions to targeted cells expressing a receptor for a polypeptide of the invention, or cells expressing a cell bound form of a polypeptide of the invention.
As discussed herein, polypeptides or antibodies of the invention may be associated with heterologous polypeptides, heterologous nucleic acids, toxins, or prodrugs via hydrophobic, hydrophilic, ionic and/or covalent interactions. In one embodiment, the invention provides a method for the specific delivery of compositions of the invention to cells by administering polypeptides of the invention (including antibodies) that are associated with heterologous polypeptides or nucleic acids. In one example, the invention provides a method for delivering a therapeutic protein into the targeted cell. In another example, the invention provides a method for delivering a single stranded nucleic acid (e.g., antisense or ribozymes) or double stranded nucleic acid (e.g., DNA that can integrate into the cell""s genome or replicate episomally and that can be transcribed) into the targeted cell.
In another embodiment, the invention provides a method for the specific destruction of cells (e.g., the destruction of tumor cells) by administering polypeptides of the invention (e.g., polypeptides of the invention or antibodies of the invention) in association with toxins or cytotoxic prodrugs.
By xe2x80x9ctoxinxe2x80x9d is meant compounds that bind and activate endogenous cytotoxic effector systems, radioisotopes, holotoxins, modified toxins, catalytic subunits of toxins, or any molecules or enzymes not normally present in or on the surface of a cell that under defined conditions cause the cell""s death. Toxins that may be used according to the methods of the invention include, but are not limited to, radioisotopes known in the art, compounds such as, for example, antibodies (or complement fixing containing portions thereof) that bind an inherent or induced endogenous cytotoxic effector system, thymidine kinase, endonuclease, RNAse, alpha toxin, ricin, abrin, Pseudomonas exotoxin A, diphtheria toxin, saporin, momordin, gelonin, pokeweed antiviral protein, alpha-sarcin and cholera toxin. By xe2x80x9ccytotoxic prodrugxe2x80x9d is meant a non-toxic compound that is converted by an enzyme, normally present in the cell, into a cytotoxic compound. Cytotoxic prodrugs that may be used according to the methods of the invention include, but are not limited to, glutamyl derivatives of benzoic acid mustard alkylating agent, phosphate derivatives of etoposide or mitomycin C, cytosine arabinoside, daunorubisin, and phenoxyacetamide derivatives of doxorubicin.
Drug Screening
Further contemplated is the use of the polypeptides of the present invention, or the polynucleotides encoding these polypeptides, to screen for molecules which modify the activities of the polypeptides of the present invention. Such a method would include contacting the polypeptide of the present invention with a selected compound(s) suspected of having antagonist or agonist activity, and assaying the activity of these polypeptides following binding.
This invention is particularly useful for screening therapeutic compounds by using the polypeptides of the present invention, or binding fragments thereof, in any of a variety of drug screening techniques. The polypeptide or fragment employed in such a test may be affixed to a solid support, expressed on a cell surface, free in solution, or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or fragment. Drugs are screened against such transformed cells in competitive binding assays. One may measure, for example, the formulation of complexes between the agent being tested and a polypeptide of the present invention.
Thus, the present invention provides methods of screening for drugs or any other agents which affect activities mediated by the polypeptides of the present invention. These methods comprise contacting such an agent with a polypeptide of the present invention or a fragment thereof and assaying for the presence of a complex between the agent and the polypeptide or a fragment thereof, by methods well known in the art. In such a competitive binding assay, the agents to screen are typically labeled. Following incubation, free agent is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of a particular agent to bind to the polypeptides of the present invention.
Another technique for drug screening provides high throughput screening for compounds having suitable binding affinity to the polypeptides of the present invention, and is described in great detail in European Patent Application 84/03564, published on Sep. 13, 1984, which is incorporated herein by reference herein. Briefly stated, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. The peptide test compounds are reacted with polypeptides of the present invention and washed. Bound polypeptides are then detected by methods well known in the art. Purified polypeptides are coated directly onto plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing antibodies may be used to capture the peptide and immobilize it on the solid support.
This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding polypeptides of the present invention specifically compete with a test compound for binding to the polypeptides or fragments thereof. In this manner, the antibodies are used to detect the presence of any peptide which shares one or more antigenic epitopes with a polypeptide of the invention.
Polypeptides of the Invention Binding Peptides and Other Molecules
The invention also encompasses screening methods for identifying polypeptides and nonpolypeptides that bind polypeptides of the invention, and the polypeptide of the invention binding molecules identified thereby. These binding molecules are useful, for example, as agonists and antagonists of the polypeptides of the invention. Such agonists and antagonists can be used, in accordance with the invention, in the therapeutic embodiments described in detail, below.
This method comprises the steps of:
a. contacting a polypeptide of the invention with a plurality of molecules; and
b. identifying a molecule that binds the polypeptide of the invention.
The step of contacting the polypeptide of the invention with the plurality of molecules may be effected in a number of ways. For example, one may contemplate immobilizing the polypeptide of the invention on a solid support and bringing a solution of the plurality of molecules in contact with the immobilized polypeptide of the invention. Such a procedure would be akin to an affinity chromatographic process, with the affinity matrix being comprised of the immobilized polypeptide of the invention. The molecules having a selective affinity for the polypeptide of the invention can then be purified by affinity selection. The nature of the solid support, process for attachment of the polypeptide of the invention to the solid support, solvent, and conditions of the affinity isolation or selection are largely conventional and well known to those of ordinary skill in the art.
Alternatively, one may also separate a plurality of polypeptides into substantially separate fractions comprising a subset of or individual polypeptides. For instance, one can separate the plurality of polypeptides by gel electrophoresis, column chromatography, or like method known to those of ordinary skill for the separation of polypeptides. The individual polypeptides can also be produced by a transformed host cell in such a way as to be expressed on or about its outer surface (e.g., a recombinant phage). Individual isolates can then be xe2x80x9cprobedxe2x80x9d by the polypeptide of the invention, optionally in the presence of an inducer should one be required for expression, to determine if any selective affinity interaction takes place between the polypeptide of the invention and the individual clone. Prior to contacting the polypeptide of the invention with each fraction comprising individual polypeptides, the polypeptides could first be transferred to a solid support for additional convenience. Such a solid support may simply be a piece of filter membrane, such as one made of nitrocellulose or nylon. In this manner, positive clones could be identified from a collection of transformed host cells of an expression library, which harbor a DNA construct encoding a polypeptide having a selective affinity for a polypeptide of the invention. Furthermore, the amino acid sequence of the polypeptide having a selective affinity for the polypeptide of the invention can be determined directly by conventional means or the coding sequence of the DNA encoding the polypeptide can frequently be determined more conveniently. The primary sequence can then be deduced from the corresponding DNA sequence. If the amino acid sequence is to be determined from the polypeptide itself, one may use microsequencing techniques. The sequencing technique may include mass spectroscopy.
In certain situations, it may be desirable to wash away any unbound polypeptide of the invention, or alterntatively, unbound polypeptides, from a mixture of the polypeptide of the invention and the plurality of polypeptides prior to attempting to determine or to detect the presence of a selective affinity interaction. Such a wash step may be particularly desirable when the polypeptide of the invention or the plurality of polypeptides is bound to a solid support.
The plurality of molecules provided according to this method may be provided by way of diversity libraries, such as random or combinatorial peptide or nonpeptide libraries which can be screened for molecules that specifically bind to a polypeptide of the invention. Many libraries are known in the art that can be used, e.g., chemically synthesized libraries, recombinant (e.g., phage display libraries), and in vitro translation-based libraries. Examples of chemically synthesized libraries are described in Fodor et al., 1991, Science 251:767-773; Houghten et al., 1991, Nature 354:84-86; Lam et al., 1991, Nature 354:82-84; Medynski, 1994, Bio/Technology 12:709-710; Gallop et al., 1994, J. Medicinal Chemistry 37(9):1233-1251; Ohlmeyer et al., 1993, Proc. Natl. Acad. Sci. USA 90:10922-10926; Erb et al., 1994, Proc. Natl. Acad. Sci. USA 91:11422-11426; Houghten et al., 1992, Biotechniques 13:412; Jayawickreme et al., 1994, Proc. Natl. Acad. Sci. USA 91:1614-1618; Salmon et al., 1993, Proc. Natl. Acad. Sci. USA 90:11708-11712; PCT Publication No. WO 93/20242; and Brenner and Lerner, 1992, Proc. Natl. Acad. Sci. USA 89:5381-5383.
Examples of phage display libraries are described in Scott and Smith, 1990, Science 249:386-390; Devlin et al., 1990, Science, 249:404-406; Christian, R. B., et al., 1992, J. Mol. Biol. 227:711-718); Lenstra, 1992, J. Immunol. Meth. 152:149-157; Kay et al., 1993, Gene 128:59-65; and PCT Publication No. WO 94/18318 dated Aug. 18, 1994.
In vitro translation-based libraries include but are not limited to those described in PCT Publication No. WO 91/05058 dated Apr. 18, 1991; and Mattheakis et al., 1994, Proc. Natl. Acad. Sci. USA 91:9022-9026.
By way of examples of nonpeptide libraries, a benzodiazepine library (see e.g., Bunin et al., 1994, Proc. Natl. Acad. Sci. USA 91:4708-4712) can be adapted for use. Peptoid libraries (Simon et al., 1992, Proc. Natl. Acad. Sci. USA 89:9367-9371) can also be used. Another example of a library that can be used, in which the amide functionalities in peptides have been permethylated to generate a chemically transformed combinatorial library, is described by Ostresh et al. (1994, Proc. Natl. Acad. Sci. USA 91:11138-11142).
The variety of non-peptide libraries that are useful in the present invention is great. For example, Ecker and Crooke, 1995, Bio/Technology 13:351-360 list benzodiazepines, hydantoins, piperazinediones, biphenyls, sugar analogs, beta-mercaptoketones, arylacetic acids, acylpiperidines, benzopyrans, cubanes, xanthines, aminimides, and oxazolones as among the chemical species that form the basis of various libraries.
Non-peptide libraries can be classified broadly into two types: decorated monomers and oligomers. Decorated monomer libraries employ a relatively simple scaffold structure upon which a variety functional groups is added. Often the scaffold will be a molecule with a known useful pharmacological activity. For example, the scaffold might be the benzodiazepine structure.
Non-peptide oligomer libraries utilize a large number of monomers that are assembled together in ways that create new shapes that depend on the order of the monomers. Among the monomer units that have been used are carbamates, pyrrolinones, and morpholinos. Peptoids, peptide-like oligomers in which the side chain is attached to the alpha amino group rather than the alpha carbon, form the basis of another version of non-peptide oligomer libraries. The first non-peptide oligomer libraries utilized a single type of monomer and thus contained a repeating backbone. Recent libraries have utilized more than one monomer, giving the libraries added flexibility.
Screening the libraries can be accomplished by any of a variety of commonly known methods. See, e.g., the following references, which disclose screening of peptide libraries: Parmley and Smith, 1989, Adv. Exp. Med. Biol. 251:215-218; Scott and Smith, 1990, Science 249:386-390; Fowlkes et al., 1992; BioTechniques 13:422-427; Oldenburg et al., 1992, Proc. Natl. Acad. Sci. USA 89:5393-5397; Yu et al., 1994, Cell 76:933-945; Staudt et al., 1988, Science 241:577-580; Bock et al., 1992, Nature 355:564-566; Tuerk et al., 1992, Proc. Natl. Acad. Sci. USA 89:6988-6992; Ellington et al., 1992, Nature 355:850-852; U.S. Pat. No. 5,096,815, U.S. Pat. No. 5,223,409, and U.S. Pat. No. 5,198,346, all to Ladner et al.; Rebar and Pabo, 1993, Science 263:671-673; and CT Publication No. WO 94/18318.
In a specific embodiment, screening to identify a molecule that binds a polypeptide of the invention can be carried out by contacting the library members with a polypeptide of the invention immobilized on a solid phase and harvesting those library members that bind to the polypeptide of the invention. Examples of such screening methods, termed xe2x80x9cpanningxe2x80x9d techniques are described by way of example in Parmley and Smith, 1988, Gene 73:305-318; Fowlkes et al., 1992, BioTechniques 13:422-427; PCT Publication No. WO 94/18318; and in references cited herein.
In another embodiment, the two-hybrid system for selecting interacting proteins in yeast (Fields and Song, 1989, Nature 340:245-246; Chien et al., 1991, Proc. Natl. Acad. Sci. USA 88:9578-9582) can be used to identify molecules that specifically bind to a polypeptide of the invention.
Where the polypeptide of the invention binding molecule is a polypeptide, the polypeptide can be conveniently selected from any peptide library, including random peptide libraries, combinatorial peptide libraries, or biased peptide libraries. The term xe2x80x9cbiasedxe2x80x9d is used herein to mean that the method of generating the library is manipulated so as to restrict one or more parameters that govern the diversity of the resulting collection of molecules, in this case peptides.
Thus, a truly random peptide library would generate a collection of peptides in which the probability of finding a particular amino acid at a given position of the peptide is the same for all 20 amino acids. A bias can be introduced into the library, however, by specifying, for example, that a lysine occur every fifth amino acid or that positions 4, 8, and 9 of a decapeptide library be fixed to include only arginine. Clearly, many types of biases can be contemplated, and the present invention is not restricted to any particular bias. Furthermore, the present invention contemplates specific types of peptide libraries, such as phage displayed peptide libraries and those that utilize a DNA construct comprising a lambda phage vector with a DNA insert.
As mentioned above, in the case of a polypeptide of the invention binding molecule that is a polypeptide, the polypeptide may have about 6 to less than about 60 amino acid residues, preferably about 6 to about 10 amino acid residues, and most preferably, about 6 to about 22 amino acids. In another embodiment, a polypeptide of the invention binding polypeptide has in the range of 15-100 amino acids, or 20-50 amino acids.
The selected polypeptide of the invention binding polypeptide can be obtained by chemical synthesis or recombinant expression.
Antisense And Ribozyme (Antagonists)
In specific embodiments, antagonists according to the present invention are nucleic acids corresponding to the sequences contained in SEQ ID NO:X, or the complementary strand thereof, and/or to nucleotide sequences contained a deposited clone. In one embodiment, antisense sequence is generated internally by the organism, in another embodiment, the antisense sequence is separately administered (see, for example, O""Connor, Neurochem., 56:560 (1991). Oligodeoxynucleotides as Anitsense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Antisense technology can be used to control gene expression through antisense DNA or RNA, or through triple-helix formation. Antisense techniques are discussed for example, in Okano, Neurochem., 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple helix formation is discussed in, for instance, Lee et al., Nucleic Acids Research, 6:3073 (1979); Cooney et al., Science, 241:456 (1988); and Dervan et al., Science, 251:1300 (1991). The methods are based on binding of a polynucleotide to a complementary DNA or RNA.
For example, the use of c-myc and c-myb antisense RNA constructs to inhibit the growth of the non-lymphocytic leukemia cell line HL-60 and other cell lines was previously described. (Wickstrom et al. (1988); Anfossi et al. (1989)). These experiments were performed in vitro by incubating cells with the oligoribonucleotide. A similar procedure for in vivo use is described in WO 91/15580. Briefly, a pair of oligonucleotides for a given antisense RNA is produced as follows: A sequence complimentary to the first 15 bases of the open reading frame is flanked by an EcoR1 site on the 5 end and a HindIII site on the 3 end. Next, the pair of oligonucleotides is heated at 90xc2x0 C. for one minute and then annealed in 2xc3x97ligation buffer (2 mM TRIS HCl pH 7.5, 10 mM MgCl2, 10 MM dithiothreitol (DTT) and 0.2 mM ATP) and then ligated to the EcoR1/Hind III site of the retroviral vector PMV7 (WO 91/15580).
For example, the 5xe2x80x2 coding portion of a polynucleotide that encodes the mature polypeptide of the present invention may be used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription thereby preventing transcription and the production of the receptor. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into receptor polypeptide.
In one embodiment, the antisense nucleic acid of the invention is produced intracellularly by transcription from an exogenous sequence. For example, a vector or a portion thereof, is transcribed, producing an antisense nucleic acid (RNA) of the invention. Such a vector would contain a sequence encoding the antisense nucleic acid of the invention. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in vertebrate cells. Expression of the sequence encoding a polypeptide of the invention, or fragments thereof, can be by any promoter known in the art to act in vertebrate, preferably human cells. Such promoters can be inducible or constitutive. Such promoters include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, Nature, 29:304-310 (1981), the promoter contained in the 3xe2x80x2 long terminal repeat of Rous sarcoma virus (Yamamoto et al., Cell, 22:787-797 (1980), the herpes thymidine promoter (Wagner et al., Proc. Natl. Acad. Sci. U.S.A., 78:1441-1445 (1981), the regulatory sequences of the metallothionein gene (Brinster et al., Nature, 296:39-42 (1982)), etc.
The antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of an RNA transcript of a gene of interest. However, absolute complementarity, although preferred, is not required. A sequence xe2x80x9ccomplementary to at least a portion of an RNA,xe2x80x9d referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double stranded antisense nucleic acids of the invention, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid Generally, the larger the hybridizing nucleic acid, the more base mismatches with a RNA sequence of the invention it may contain and still form a stable duplex (or triplex as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.
Oligonucleotides that are complementary to the 5xe2x80x2 end of the message, e.g., the 5xe2x80x2 untranslated sequence up to and including the AUG initiation codon, should work most efficiently at inhibiting translation. However, sequences complementary to the 3xe2x80x2 untranslated sequences of mRNAs have been shown to be effective at inhibiting translation of mRNAs as well. See generally, Wagner, R., Nature, 372:333-335 (1994). Thus, oligonucleotides complementary to either the 5xe2x80x2- or 3xe2x80x2-non-translated, non-coding regions of a polynucleotide sequence of the invention could be used in an antisense approach to inhibit translation of endogenous mRNA. Oligonucleotides complementary to the 5xe2x80x2 untranslated region of the mRNA should include the complement of the AUG start codon. Antisense oligonucleotides complementary to mRNA coding regions are less efficient inhibitors of translation but could be used in accordance with the invention. Whether designed to hybridize to the 5xe2x80x2-, 3xe2x80x2- or coding region of mRNA, antisense nucleic acids should be at least six nucleotides in length, and are preferably oligonucleotides ranging from 6 to about 50 nucleotides in length. In specific aspects the oligonucleotide is at least 10 nucleotides, at least 17 nucleotides, at least 25 nucleotides or at least 50 nucleotides.
The polynucleotides of the invention can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, hybridization, etc. The oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556 (1989); Lemaitre et al., Proc. Natl. Acad. Sci., 84:648-652 (1987); PCT Publication NO: WO88/09810, published Dec. 15, 1988) or the blood-brain barrier (see, e.g., PCT Publication NO: WO89/10134, published Apr. 25, 1988), hybridization-triggered cleavage agents. (See, e.g., Krol et al., BioTechniques, 6:958-976 (1988)) or intercalating agents. (See, e.g., Zon, Pharm. Res., 5:539-549 (1988)). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent, etc.
The antisense oligonucleotide may comprise at least one modified base moiety which is selected from the group including, but not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5xe2x80x2-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, (acp3)w, and 2,6-diaminopurine.
The antisense oligonucleotide may also comprise at least one modified sugar moiety selected from the group including, but not limited to, arabinose, 2-fluoroarabinose, xylulose, and hexose.
In yet another embodiment, the antisense oligonucleotide comprises at least one modified phosphate backbone selected from the group including, but not limited to, a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof.
In yet another embodiment, the antisense oligonucleotide is an a-anomeric oligonucleotide. An a-anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gautier et al., Nucl. Acids Res., 15:6625-6641 (1987)). The oligonucleotide is a 2-0-methylribonucleotide (Inoue et al., Nucl. Acids Res., 15:6131-6148 (1987)), or a chimeric RNA-DNA analogue (Inoue et al., FEBS Lett. 215:327-330 (1987)).
Polynucleotides of the invention may be synthesized by standard methods known in the art, e.g. by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc.). As examples, phosphorothioate oligonucleotides may be synthesized by the method of Stein et al. (Nucl. Acids Res., 16:3209 (1988)), methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports (Sarin et al., Proc. Natl. Acad. Sci. U.S.A., 85:7448-7451 (1988)), etc.
While antisense nucleotides complementary to the coding region sequence of the invention could be used, those complementary to the transcribed untranslated region are most preferred.
Potential antagonists according to the invention also include catalytic RNA, or a ribozyme (See, e.g., PCT International Publication WO 90/11364, published Oct. 4, 1990; Sarver et al, Science, 247:1222-1225 (1990). While ribozymes that cleave mRNA at site specific recognition sequences can be used to destroy mRNAs corresponding to the polynucleotides of the invention, the use of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target mRNA have the following sequence of two bases: 5xe2x80x2-UG-3xe2x80x2. The construction and production of hammerhead ribozymes is well known in the art and is described more fully in Haseloff and Gerlach, Nature, 334:585-591 (1988). There are numerous potential hammerhead ribozyme cleavage sites within each nucleotide sequence disclosed in the sequence listing. Preferably, the ribozyme is engineered so that the cleavage recognition site is located near the 5xe2x80x2 end of the mRNA corresponding to the polynucleotides of the invention; i.e., to increase efficiency and minimize the intracellular accumulation of non-functional mRNA transcripts.
As in the antisense approach, the ribozymes of the invention can be composed of modified oligonucleotides (e.g. for improved stability, targeting, etc.) and should be delivered to cells which express the polynucleotides of the invention in vivo. DNA constructs encoding the ribozyme may be introduced into the cell in the same manner as described above for the introduction of antisense encoding DNA. A preferred method of delivery involves using a DNA construct xe2x80x9cencodingxe2x80x9d the ribozyme under the control of a strong constitutive promoter, such as, for example, pol III or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to destroy endogenous messages and inhibit translation. Since ribozymes unlike antisense molecules, are catalytic, a lower intracellular concentration is required for efficiency.
Antagonist/agonist compounds may be employed to inhibit the cell growth and proliferation effects of the polypeptides of the present invention on neoplastic cells and tissues, i.e. stimulation of angiogenesis of tumors, and, therefore, retard or prevent abnormal cellular growth and proliferation, for example, in tumor formation or growth.
The antagonist/agonist may also be employed to prevent hyper-vascular diseases, and prevent the proliferation of epithelial lens cells after extracapsular cataract surgery. Prevention of the mitogenic activity of the polypeptides of the present invention may also be desirous in cases such as restenosis after balloon angioplasty.
The antagonist/agonist may also be employed to prevent the growth of scar tissue during wound healing.
The antagonist/agonist may also be employed to treat, prevent, and/or diagnose the diseases described herein.
Thus, the invention provides a method of treating or preventing diseases, disorders, and/or conditions, including but not limited to the diseases, disorders, and/or conditions listed throughout this application, associated with overexpression of a polynucleotide of the present invention by administering to a patient (a) an antisense molecule directed to the polynucleotide of the present invention, and/or (b) a ribozyme directed to the polynucleotide of the present invention. invention, and/or (b) a ribozyme directed to the polynucleotide of the present invention
Other Activities
The polypeptide of the present invention, as a result of the ability to stimulate vascular endothelial cell growth, may be employed in treatment for stimulating re-vascularization of ischemic tissues due to various disease conditions such as thrombosis, arteriosclerosis, and other cardiovascular conditions. These polypeptide may also be employed to stimulate angiogenesis and limb regeneration, as discussed above.
The polypeptide may also be employed for treating wounds due to injuries, burns, post-operative tissue repair, and ulcers since they are mitogenic to various cells of different origins, such as fibroblast cells and skeletal muscle cells, and therefore, facilitate the repair or replacement of damaged or diseased tissue.
The polypeptide of the present invention may also be employed stimulate neuronal growth and to treat, prevent, and/or diagnose neuronal damage which occurs in certain neuronal disorders or neuro-degenerative conditions such as Alzheimer""s disease, Parkinson""s disease, and AIDS-related complex. The polypeptide of the invention may have the ability to stimulate chondrocyte growth, therefore, they may be employed to enhance bone and periodontal regeneration and aid in tissue transplants or bone grafts.
The polypeptide of the present invention may be also be employed to prevent skin aging due to sunburn by stimulating keratinocyte growth.
The polypeptide of the invention may also be employed for preventing hair loss, since FGF family members activate hair-forming cells and promotes melanocyte growth. Along the same lines, the polypeptides of the present invention may be employed to stimulate growth and differentiation of hematopoietic cells and bone marrow cells when used in combination with other cytokines.
The polypeptide of the invention may also be employed to maintain organs before transplantation or for supporting cell culture of primary tissues.
The polypeptide of the present invention may also be employed for inducing tissue of mesodermal origin to differentiate in early embryos.
The polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also increase or decrease the differentiation or proliferation of embryonic stem cells, besides, as discussed above, hematopoietic lineage.
The polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used to modulate mammalian characteristics, such as body height, weight, hair color, eye color, skin, percentage of adipose tissue, pigmentation, size, and shape (e.g., cosmetic surgery). Similarly, polypeptides or polynucleotides and/or agonist or antagonists of the present invention may be used to modulate mammalian metabolism affecting catabolism, anabolism, processing, utilization, and storage of energy.
Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may be used to change a mammal""s mental state or physical state by influencing biorhythms, caricadic rhythms, depression (including depressive diseases, disorders, and/or conditions), tendency for violence, tolerance for pain, reproductive capabilities (preferably by Activin or Inhibin-like activity), hormonal or endocrine levels, appetite, libido, memory, stress, or other cognitive qualities.
Polypeptide or polynucleotides and/or agonist or antagonists of the present invention may also be used as a food additive or preservative, such as to increase or decrease storage capabilities, fat content, lipid, protein, carbohydrate, vitamins, minerals, cofactors or other nutritional components.
Other Preferred Embodiments
Other preferred embodiments of the claimed invention include an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a sequence of at least about 50 contiguous nucleotides in the nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1.
Also preferred is a nucleic acid molecule wherein said sequence of contiguous nucleotides is included in the nucleotide sequence of SEQ ID NO:X in the range of positions beginning with the nucleotide at about the position of the 5xe2x80x2 Nucleotide of the Clone Sequence and ending with the nucleotide at about the position of the 3xe2x80x2 Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
Also preferred is a nucleic acid molecule wherein said sequence of contiguous nucleotides is included in the nucleotide sequence of SEQ ID NO:X in the range of positions beginning with the nucleotide at about the position of the 5xe2x80x2 Nucleotide of the Start Codon and ending with the nucleotide at about the position of the 3xe2x80x2 Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
Similarly preferred is a nucleic acid molecule wherein said sequence of contiguous nucleotides is included in the nucleotide sequence of SEQ ID NO:X in the range of positions beginning with the nucleotide at about the position of the 5xe2x80x2 Nucleotide of the First Amino Acid of the Signal Peptide and ending with the nucleotide at about the position of the 3xe2x80x2 Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a sequence of at least about 150 contiguous nucleotides in the nucleotide sequence of SEQ ID NO:X.
Further preferred is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a sequence of at least about 500 contiguous nucleotides in the nucleotide sequence of SEQ ID NO:X.
A further preferred embodiment is a nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NO:X beginning with the nucleotide at about the position of the 5xe2x80x2 Nucleotide of the First Amino Acid of the Signal Peptide and ending with the nucleotide at about the position of the 3xe2x80x2 Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
A further preferred embodiment is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to the complete nucleotide sequence of SEQ ID NO:X.
Also preferred is an isolated nucleic acid molecule which hybridizes under stringent hybridization conditions to a nucleic acid molecule, wherein said nucleic acid molecule which hybridizes does not hybridize under stringent hybridization conditions to a nucleic acid molecule having a nucleotide sequence consisting of only A residues or of only T residues.
Also preferred is a composition of matter comprising a DNA molecule which comprises a human cDNA clone identified by a cDNA Clone Identifier in Table 1, which DNA molecule is contained in the material deposited with the American Type Culture Collection and given the ATCC(copyright) Deposit Number shown in Table 1 for said cDNA Clone Identifier.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a sequence of at least 50 contiguous nucleotides in the nucleotide sequence of a human cDNA clone identified by a cDNA Clone Identifier in Table 1, which DNA molecule is contained in the deposit given the ATCC(copyright) Deposit Number shown in Table 1.
Also preferred is an isolated nucleic acid molecule, wherein said sequence of at least 50 contiguous nucleotides is included in the nucleotide sequence of the complete open reading frame sequence encoded by said human cDNA clone.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to sequence of at least 150 contiguous nucleotides in the nucleotide sequence encoded by said human cDNA clone.
A further preferred embodiment is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to sequence of at least 500 contiguous nucleotides in the nucleotide sequence encoded by said human cDNA clone.
A further preferred embodiment is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to the complete nucleotide sequence encoded by said human cDNA clone.
A further preferred embodiment is a method for detecting in a biological sample a nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1; and a nucleotide sequence encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1; which method comprises a step of comparing a nucleotide sequence of at least one nucleic acid molecule in said sample with a sequence selected from said group and determining whether the sequence of said nucleic acid molecule in said sample is least 95% identical to said selected sequence.
Also preferred is the above method wherein said step of comparing sequences comprises determining the extent of nucleic acid hybridization between nucleic acid molecules in said sample and a nucleic acid molecule comprising said sequence selected from said group. Similarly, also preferred is the above method wherein said step of comparing sequences is performed by comparing the nucleotide sequence determined from a nucleic acid molecule in said sample with said sequence selected from said group. The nucleic acid molecules can comprise DNA molecules or RNA molecules.
A further preferred embodiment is a method for identifying the species, tissue or cell type of a biological sample which method comprises a step of detecting nucleic acid molecules in said sample, if any, comprising a nucleotide sequence that is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1; and a nucleotide sequence encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
The method for identifying the species, tissue or cell type of a biological sample can comprise a step of detecting nucleic acid molecules comprising a nucleotide sequence in a panel of at least two nucleotide sequences, wherein at least one sequence in said panel is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from said group.
Also preferred is a method for diagnosing in a subject a pathological condition associated with abnormal structure or expression of a gene encoding a secreted protein identified in Table 1, which method comprises a step of detecting in a biological sample obtained from said subject nucleic acid molecules, if any, comprising a nucleotide sequence that is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1; and a nucleotide sequence encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
The method for diagnosing a pathological condition can comprise a step of detecting nucleic acid molecules comprising a nucleotide sequence in a panel of at least two nucleotide sequences, wherein at least one sequence in said panel is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from said group.
Also preferred is a composition of matter comprising isolated nucleic acid molecules wherein the nucleotide sequences of said nucleic acid molecules comprise a panel of at least two nucleotide sequences, wherein at least one sequence in said panel is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1; and a nucleotide sequence encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1. The nucleic acid molecules can comprise DNA molecules or RNA molecules.
Also preferred is an isolated polypeptide comprising an amino acid sequence at least 90% identical to a sequence of at least about 10 contiguous amino acids in the amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1.
Also preferred is a polypeptide, wherein said sequence of contiguous amino acids is included in the amino acid sequence of SEQ ID NO:Y in the range of positions beginning with the residue at about the position of the First Amino Acid of the Secreted Portion and ending with the residue at about the Last Amino Acid of the Open Reading Frame as set forth for SEQ ID NO:Y in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to a sequence of at least about 30 contiguous amino acids in the amino acid sequence of SEQ ID NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to a sequence of at least about 100 contiguous amino acids in the amino acid sequence of SEQ ID NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to the complete amino acid sequence of SEQ ID NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid sequence at least 90% identical to a sequence of at least about 10 contiguous amino acids in the complete amino acid sequence of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is a polypeptide wherein said sequence of contiguous amino acids is included in the amino acid sequence of a secreted portion of the secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to a sequence of at least about 30 contiguous amino acids in the amino acid sequence of the secreted portion of the protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to a sequence of at least about 100 contiguous amino acids in the amino acid sequence of the secreted portion of the protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence at least 95% identical to the amino acid sequence of the secreted portion of the protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Further preferred is an isolated antibody which binds specifically to a polypeptide comprising an amino acid sequence that is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Further preferred is a method for detecting in a biological sample a polypeptide comprising an amino acid sequence which is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1; which method comprises a step of comparing an amino acid sequence of at least one polypeptide molecule in said sample with a sequence selected from said group and determining whether the sequence of said polypeptide molecule in said sample is at least 90% identical to said sequence of at least 10 contiguous amino acids.
Also preferred is the above method wherein said step of comparing an amino acid sequence of at least one polypeptide molecule in said sample with a sequence selected from said group comprises determining the extent of specific binding of polypeptides in said sample to an antibody which binds specifically to a polypeptide comprising an amino acid sequence that is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is the above method wherein said step of comparing sequences is performed by comparing the amino acid sequence determined from a polypeptide molecule in said sample with said sequence selected from said group.
Also preferred is a method for identifying the species, tissue or cell type of a biological sample which method comprises a step of detecting polypeptide molecules in said sample, if any, comprising an amino acid sequence that is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is the above method for identifying the species, tissue or cell type of a biological sample, which method comprises a step of detecting polypeptide molecules comprising an amino acid sequence in a panel of at least two amino acid sequences, wherein at least one sequence in said panel is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the above group.
Also preferred is a method for diagnosing in a subject a pathological condition associated with abnormal structure or expression of a gene encoding a secreted protein identified in Table 1, which method comprises a step of detecting in a biological sample obtained from said subject polypeptide molecules comprising an amino acid sequence in a panel of at least two amino acid sequences, wherein at least one sequence in said panel is at least 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
In any of these methods, the step of detecting said polypeptide molecules includes using an antibody.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a nucleotide sequence encoding a polypeptide wherein said polypeptide comprises an amino acid sequence that is at east 90% identical to a sequence of at least 10 contiguous amino acids in a sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Also preferred is an isolated nucleic acid molecule, wherein said nucleotide sequence encoding a polypeptide has been optimized for expression of said polypeptide in a prokaryotic host.
Also preferred is an isolated nucleic acid molecule, wherein said polypeptide comprises an amino acid sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and a complete amino acid sequence of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1.
Further preferred is a method of making a recombinant vector comprising inserting any of the above isolated nucleic acid molecule into a vector. Also preferred is the recombinant vector produced by this method. Also preferred is a method of making a recombinant host cell comprising introducing the vector into a host cell, as well as the recombinant host cell produced by this method.
Also preferred is a method of making an isolated polypeptide comprising culturing this recombinant host cell under conditions such that said polypeptide is expressed and recovering said polypeptide. Also preferred is this method of making an isolated polypeptide, wherein said recombinant host cell is a eukaryotic cell and said polypeptide is a secreted portion of a human secreted protein comprising an amino acid sequence selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y beginning with the residue at the position of the First Amino Acid of the Secreted Portion of SEQ ID NO:Y wherein Y is an integer set forth in Table 1 and said position of the First Amino Acid of the Secreted Portion of SEQ ID NO:Y is defined in Table 1; and an amino acid sequence of a secreted portion of a protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in the deposit with the ATCC(copyright) Deposit Number shown for said cDNA clone in Table 1. The isolated polypeptide produced by this method is also preferred.
Also preferred is a method of treatment of an individual in need of an increased level of a secreted protein activity, which method comprises administering to such an individual a pharmaceutical composition comprising an amount of an isolated polypeptide, polynucleotide, or antibody of the claimed invention effective to increase the level of said protein activity in said individual.
The above-recited applications have uses in a wide variety of hosts. Such hosts include, but are not limited to, human, murine, rabbit, goat, guinea pig, camel, horse, mouse, rat, hamster, pig, micro-pig, chicken, goat, cow, sheep, dog, cat, non-human primate, and human. In specific embodiments, the host is a mouse, rabbit, goat, guinea pig, chicken, rat, hamster, pig, sheep, dog or cat. In preferred embodiments, the host is a mammal. In most preferred embodiments, the host is a human.
In specific embodiments of the invention, for each xe2x80x9cContig IDxe2x80x9d listed in the fourth column of Table 6, preferably excluded are one or more polynucleotides comprising, or alternatively consisting of, a nucleotide sequence referenced in the fifth column of Table 6 and described by the general formula of a-b, whereas a and b are uniquely determined for the corresponding SEQ ID NO:X referred to in column 3 of Table 6. Further specific embodiments are directed to polynucleotide sequences excluding one, two, three, four, or more of the specific polynucleotide sequences referred to in the fifth column of Table 6. In no way is this listing meant to encompass all of the sequences which may be excluded by the general formula, it is just a representative example. All references available through these accessions are hereby incorporated by reference in their entirety.
Having generally described the invention, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting.